It won't let me put down a flag over a mountain even though they touch. it says "flag must connect to territory". is this a bug or am i missing something?
It could be that the mountain area is preventing the flag from being placed. Flags can't be built on lakes or mountains, stuff like that. You should see red lines for these areas. It could also be that your alliance doesn't have access to the pass that would allow your alliance to build in that zone. Otherwise it may be a bug.