I've found the issue and fixed it in the new v096. I had a really terrible workflow from Blender > Unity and at one point all world objects lost their tags, layer settings, extra components, colliders, navmesh settings etc. It was a bit of a last minute crazy panic adding them all back in haha. Looks like I missed a few bits on those farming thingos as their tops were stilll considered walkable. Thanks for reporting it! So glad to hear you're enjoying the game!
edit: Hopefully this shouldn't happen again, but if something similar occurs, the 'destroy enemy' button on the debug menu will instantly destroy the last enemy you hit.