First-half goals by David Ball and Alan Goodall did the damage, with Vale winger Jennison Myrie-Williams seeing his second-half penalty saved by 'keeper Scott Davies.
"We were second best throughout the game. It was a tired performance and we looked jaded," said Adams, whose side lost top spot in League Two.
"We started reasonably well and Tom (Pope) will be disappointed he didn't put at least one of his chances away, but it wasn't our day.
"I could make all the usual excuses because we have done a lot of travelling for two away games while Fleetwood have had two at home. That might have made a difference and it might not.
"There can certainly be no excuses for conceding from two set-plays. As a unit Fleetwood aren't a big side and it was very disappointing to concede like that.
"But Fleetwood played very, very well and what we have to do after this is regroup and see if we can put in a much brighter performance against Plymouth on Saturday."