Ireland were knocked out of the World Cup playoff phase in Prague on penalties after the scores had finished 2-2 after extra-time.
The Czechs won the shootout 4-3 after Finn Azaz and Alan Browne had their efforts saved by the hosts' goalkeeper Matej Kovar.
"We were in a good spot," captain Collins told BBC Sport NI.
"We were playing really well. We were front-footed, creating chances, our press was working, we were hurting them on the ball.
"The timing of their first goal probably affects it a bit and knocks the wind out of you. They had a lot to fight for in the second half, but it's probably the timing of it rather than the performance."
On Azaz and Browne, Collins also said: "They have a lot of thoughts in their head right now.
"There's not a lot you can say to a person when they're in that position. But there are not a lot of people that would stand up and take a penalty.
"It took a lot of bravery for them to do that so there's no fingers being pointed at them at all."