Hartlepool caretaker boss Mick Wadsworth was left to rue a lapse in concentration that led to Lewis Guy's winner for MK Dons.
Pools looked to be heading for a hard earned point at stadium:mk until Guy struck late on.
Wadsworth said: "I'm disappointed in the goal because I thought we defended very well until then.
"The team shape and what we tried to do worked very well.
"If you're not compact against a team like MK then they will tear you apart with their passing and their movement - but they didn't.
"They had lots of possession but we probably out-scored them on entries into the box."