When looking at the booking confirmation, be sure to check what Rate Plan was associated with the booking.  For some channels, there are certain rate plans that the channel stipulates, and that myallocator is not able to manage.  

For example:  your standard rate plan may consist of a 2-night minimum stay.  Some channels, such as booking.com, may also require you to have another rate plan, such as an Early Booker with 20% discount.  With those channel-specific rate plans, myallocator is not able to manage them and therefore the minimum night stay is not enforced.

Also, not all channels support setting minimum/maximum stay. Some channels (e.g. Hostelbookers) only support setting one minimum stay per day for all rooms so unless you have the same minimum stay for all rooms for a single day it's possible that it's set to the wrong minimum stay.

You can check out Channel Features article to find out which channels support which features.