I delved a bit further to reproduce the bugs:
- Villages not listening: this seems to happen when I (i) select the villager; (ii) select (left-click) resource A; (iii) send the villager (right-click) to resource B. In this case the villager walks to B but does not mine. It does not happen consistently like that, but I'd say at least half the time. It does not seem to happen if A == B. I guess I just have an unusual order of clicking around :-) I guess it could be the same for the soldiers.
- ghost buildings: clicking on another building button does not necessarily fix it; I often need to deselect and reselect the villager itself. I have not been able to figure out exactly what triggers it.
OS: Win 10 Pro; Intel i7, 64bit, AMD Radeon HD6900. It is curious though that the presence/absence of these functional bugs would vary between systems. Unless this functionality relies on some non-standard Godot functionality it should work the same everywhere. Any chance that the export templates you used do not match the Godot dev version you wrote it in?