Zeus/Poseidon bugs:
In regards to the Cattle ranches: It is also possible to end up with a cattle industry that won't support as many cattle as it is supposed to. This seems to happen when sanctuaries are sacrificing cattle. The sanctuaries apparently don't pay attention to the ranchers' tally of allowed cattle, meaning that the herd size slowly decreases over time. Saving and restoring solves this problem, just like the above cattle problem. No restarting the game is necessary (in my experience). I would suggest keeping cattle ranches out of episodes with sanctuaries to avoid this.
In regards to the traders not arriving in a timely manner, I've noticed this myself and did some experimentation. Waiting for extended lengths of time produced no traders, however, as soon as I would save and reload the game, the missing caravan pops up within seconds. Trade ships take longer, but always show up within a month. So, either there is a bug with caravans not showing up on time, _or_ there is a bug with the game forgetting to save the fact that the caravans aren't arriving on time and it also isn't giving a 'associated city not trading' message when caravans aren't showing. Either way, there is some sort of bug here.
Some other bugs (And yes, as far as I know, I have the latest patch):
When Zeus is attacking the city, if the palace is destroyed and repeatedly rebuilt, there is a bug whereby some of the units become confused and think that their standard is a tower or something. You can still order the units around, but their standard won't be visible. This would be okay, but for the second part of this bug: maintanence offices (and possibly other buildings) stop producing walkers. I _think_ that if the palace is deleted, they will start working again, but only so long as the palace stays deleted. This would actually almost be a cool Zeus curse (he is supposed to be nasty after all), but I am pretty sure it is a bug.
Solution: You are completely and totally screwed. Restart the scenario. To avoid, don't rebuild palace until Zeus has his fun, or rebuild it way far away, so he has to walk a long way to walk.
Roads up cliffs: If you place a road right next to a cliff, then build a boulevard on it, it places a road where the edge of the boulevard overlaps the cliff. This produces some nasty visual glitches and a road up the cliff that cannot be deleted. It also seems to allow people to walk up and down the cliff, even if the spot would otherwise be inaccessible. Of course, I consider this cheating, so don't use it.
Partially destroyed buildings: Certain buildings, when destroyed in a transitional state, may leave pieces of themselves behind. These chunks often cannot be deleted and serve as a permanent impediment. I've seen this most often with trade buildings/warehouses, when someone deposits an item at the instant the building is destroyed. The dock part of a trade wharf can also get stuck if a ship starts trying to trade at just the right instant. I even saw this with my palace once. Was really annoying to have my nice fortified compound permanently jammed up. Curse you Zeus! The only solution that I know of, other than restarting the scenario or just building around the glitched spot is to get very lucky and have a tidal wave take out the building fragment in question. This actually happened once.
A related glitch can result when a landslide falls on an operational hippodrome. Apparently, the racing horses don't notice that the hippodrome is gone soon enough and you end up with some ugly (but not harmful) visual glitches.
Speaking of landslide problems, if a landslide falls "on" a sheep or goat, the sheep or goat survives, but can be permanently embedded in the cliff wall. The only way I know of to get rid of it, so as to be able to place one that your herders can get at is to delete all the sheep/goat buildings and wait for the animals to die off, then replace the buildings and animals. Exploiting the boulevard bug listed above might also work, but I've yet to try this.
Non-invasions: If you place an invasion point in a forest, invasions won't be able to arrive there and the player will get a 'bribe for 1 drachma' option. If they choose to fight, there of course won't be any troops.
Solution: Delete the forest under the invasion point and replace with a very thick scrub square. The dark green will look the same and the invasion will arrive properly.
Poorly synchronized invasions: While coming up with nasty things to do to the player, I hit upon the idea that an enemy might approach the city, then circle around it and attack from multiple directions. To make this look/work, I tried having one invasion set with 3 months warning and the other invasions set to occur 3 months later with 0 months warning. During testing, I discovered that the invasions were sometimes arriving together and sometimes not. I threw together an experimental scenario to try to figure out what was happening. This scenario involved both 3 month warning and 0 month warning invasions every month. I gave the invasions differing numbers of men each month, so I could tell by the bribe numbers when they were supposed to arrive. After a bit of trial, I discovered that the problem seemed to be related to the start of the year not matching with the start of the scenario. If I ran the scheduled invasions in the first episode, everything worked out fine. If I copied the invasions into the second episode, ran the first episode a few months, then went into the second episode, I discovered that the timing was fine until January, at which point things went haywire and invasions started arriving at the wrong time. It might be possible to solve this problem by using a yearly production goal to end the previous episode, forcing the year and episode starts to coincide.
The above situation also revealed another bug, whereby bribing a force from a city, no matter how small the force is, bribes all troops from the city, even though you only have to pay for the group that just arrived.
Fishing docks/water crossings on flooded coastlines: When a permanent flood alters the coastline, spots that contained forests cannot be used to place fishing docks, even if the flat section of coastline _looks_ like a fishing dock should be possible there. The forest can also placement of water crossings in the newly flooded zone. Apparently, the forests are still there, but can no longer be deleted or otherwise interacted with (if you could place a water crossing, It wouldn't surprise me if you could exploit the forest for lumber though. Would be pretty funny, chopping up the water crossing for lumber).
Solution: As a player, remove forests from where the flood will be, before the flood occurs. As a scenario designer, don't put forests on the very edge of the flood zone. (The non flooded squares next to the flood zone are okay.) While you could try to use this to keep players from building on a flat stretch of flooded coastline, you can't count on the player not clearing the forests. Just don't make flat coastlines if you don't want water crossings/fishing docks there.
Lava visual glitches: Although lava can go up or down rocks just fine, it usually produces nasty visual glitches, which is probably why you don't usually see scenarios with actual cone shaped volcanoes. There actually is a workaround to this however. By placing the 'half-slope' terrain feature either on a corner, or three in a row, you can create a larger 'half-slope' rock formation, which takes the place of individual half slopes. This formation is indestructible, just like any half-slope/cliff face. It also has visual priority over a lava square, meaning you can safely run lava flows under it, allowing the creation of really neat looking volcanoes.