You can use the 'native' overlay to see if they're properly appeased. In Lugdunum there is one native hut that is a bit farther from the others that's easy to miss; if you don't give it road access as well so the missionary can walk by, they can still get angry if you build on their land (edit: not road access per se; natives don't need it, but access in a sense that a missionary walks by it on a road that's not farther than two tiles away from it). My guess is that's what caused your problem.
Otherwise - if it's not that one hut - it's just that one of the huts didn't get access for a while from the mission post. It can happen sometimes. Best to check the native overlay AND check if the missionaries are passing all the huts regularly before you build on native's land. It doesn't have to do with the weapons, believe me ;-) Weapons are great to deal with natives anywhere if you can produce them, because money'll be flying in like crazy :-)
Also, I just noticed this in your post: you don't need weapons for a Javelin fort. Only legionaires need weapons. Weapons still ARE great to sell them though!
[This message has been edited by Heleen (edited 12-28-2018 @ 01:08 PM).]