I play PA a lot, which leads me to find quite a few pathing bugs. One of the most common bugs I have encountered is that units will forget where the commander is, and clump around his previous location. Sending the 'stuck' units to a new target and then to the commander has about a 50/50 chance of working. The only way to un-stuck them is to micro them over to the commander so that they will automatically shoot him. Trying to get the units to attack the commander at this point will inevitably result in them rushing back to the commander's previous location. Even weirder still, if you select a different group of units and tell them to attack the commander, they won't rush to the 'forgotten' location; they will get close to the commander and start shooting like normal.
I agree, many of the pathing related problems I was seeing prior to the latest patch or two are still present. Units are still getting stuck around buildings, or by trying to move through the commander/fabbers in the latest ('offline') release. I'm not sure if they're still getting irretrievably stuck on terrain (e.g. metal planet when fighting the orange faction leader in GW), I'll have to check that. If units aren't allowed to clip at all, then unless they recognise that they're stuck and|or need to generate an alternative path, this problem will continue. It can be micro-managed but it's a bit of a faff to do so. Units can still get completely stuck in the gaps between buildings (this has been present since the alpha), I recently had to reclaim an energy generator so that my commander could move again. In another game, a fabber tried to walk in-between two factories and ended up irretrievably stuck so I had to delete it. Lastly, I'm not sure if this is pathing-related or not, but most of the time fabbers/the commander will not follow build queue orders when moving to build a T2 factory. The order is still in the queue, but nothing happens until you select them and issue a new command to build the factory.
I just hope that the engineers use the bug tracker because these are all there. Have been... http://pa.lennardf1989.com/Tracker/
Another thing: Units will randomly run into terrain even though they shouldn't, as if they are trying to go in a straight line.