Exosuit clearance not working as intended.

That is the intention. Dupes will not return a suit to a dock that is not vacant.
They will instead try to find another checkpoint that is free.

As for your save, the checkpoints are not being used as intended.
You have one station entering the failsafe of another station and
then they have no way of reaching the original checkpoint.

This is a proper use of Vacant setting:

 

Edited October 14, 2017 by Risu

Thanks for the clarification. Tested and working.