The Shrimps were leading through Garry Hunter but two goals from Clayton Donaldson, the second in injury time, completed Crewe's turnaround.
Lillis said: "To let Donaldson get a free header in the box is disappointing. We knew he is dangerous and we've let him score two goals against us.
"When we got the goal we thought we were going on to win it but football kicks you in the teeth and that sums up our season.
"We played ever so well and then switched off. Losing Andy Parrish to injury was a big blow and if he had stayed on I think we would have won the game.
"The boys played to the game plan and we got in their faces and created chances so to come away with a loss is a bit hard to stomach. We have to stay positive there is a game on Monday against Hereford and we can put things right there."
Source: PA
Source: PA