The title is self-explanatory. This happens when a bunch of Engineers start to build things around them and block themselves and other mercenaries or when, for example, a merc is trying to come to a dispenser but bumps into a sentry and can't come through. I understand that this is hard to make the mercenaries to be able to pathfind around the sentries and dispensers. Perhaps, the mercs from the same team as the buildings should be able to go through them.

I personally agree with this. I do completely understand that the games are designed differently, and as such Minecraft will have inherent differences, but it shouldn't be all that out there to make it so you can walk through buildings you don't own that are on your team. You can walk through boats and other entities. >.>