Esmael Goncalves scored twice as the Buddies booked their place in the quarter-finals of the William Hill Scottish Cup.
Lomas' side passed up a host of chances before Goncalves' double, and the Saints boss said: "We thought we had got over our Achilles heel in the last few games, we had looked clinical in our last two matches.
"I felt we should have went in at half-time 2-0 ahead.
"Craig Samson has made one wonderful save - that's what he's paid for, though.
"That's the difference and the reason as to why we are not second in the league just now.
"The defending for the two goals was a shambles and cost us big time."