I recently started a game where i was going to try to use almost exclusively the ninzul units. therefore, I researched the regeneration station (forget its real name but its the building that holds 500 units and repairs them at 10X their attrition rate)
Anyway, Upon gathering a huge swarm of units, which looks mighty impressive by the way, units going to dock to repair automatically were beginning to hit some issues. After one of the stations was full (all 500 units) there would be still 10 or so units in transit towards the station. Upon reaching it and noticing it was full, they would simply stop moving. I had mobile military to auto frd and this would kick them out of auto frd, Also, they would not make a second check for open slots, sitting where they ended up untill they died of attrition.
My suggestion would be to put in multiple checks in the routine which causes the units to seek out the regeneration stations. That way, if they hit a full one, a few seconds later, they would begin searching for other empty ones.