Here's an example.

My opponent attack one of my sectors where i have a zergling and a queen. Sector's unit limit is 2. He attacks me with 2 marines and a wright. Only my queen survives. And on the same planet is a free empty sector. So i must retreat, but so do my enemy, because he has 3 units in a 2-unit limit zone. Both we want to retreat to that free sector, but who goes there first ?

FAQ to the rescue:

http://new.fantasyflightgames.com/ffg_content/StarCraft/scbw_faq.pdf

Q: Who retreats first at the end of a battle if the defender
has an assist unit and the attacker is exceeding the areas,
unit limit?
A: Retreating due to exceeding stacking limits happens after
all defending units have retreated.