I've had issues before in a station defense where the allies run out of PPT and don't retreat and there are 0 PPT allied ships floating around wasting deployment points. I eventually just destroyed them because I needed more ships to defend the station, but it felt bad.
I also find it annoying when I retreat ships and the allies immediately fill that DP with small ships when I was trying to save DP to deploy big ships. If the allies are enough to win, sure it's fine, but if the allied ships are weak and causing you to take damage/lose the ships you deploy when you could win with a full deployment of your own ships, it's annoying.