Peter Weatherson had given the Greenock men a 23rd-minute lead before outstanding strikes by Paul Burns and Derek Holmes handed the Doonhamers all three points.
And with Morton now marooned in third bottom, seven points off the mid-table pack, McManus said: “It was a tough one for us to take given we had established the lead, but they were two exceptional strikes fit to win any game.
“I felt we didn’t turn up in the second half. We will need to go back to the drawing board.”
Meanwhile, Dundee continued to set the pace in the First Division with a come from behind 3-1 victory at Ayr United to stay five points clear of Queen of the South.
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