Although Billy Sharp levelled, the visitors claimed all three points thanks to a second-half strike from Gary Hart.
"It was always going to be difficult after going down to 10 men so early," he confessed.
"Foster insists there was no malice in his challenge, but the referee has made a decision.
"The two goals we conceded were both disappointing from a defensive point of view.
"After getting back on level terms just before half-time I was hoping we could go on and win it, but we could not play at the high tempo we needed and ended up having to try and change our style of play.
"Hopefully this is just a blip in form. We have been on an excellent run but how many times does this sort of result happen in a game like this when you play a team who have been struggling."
Brighton boss Dean Wilkins was relieved to end a run of four successive defeats.
"I hate losing but there were a couple of performances in that run of defeats we have had that were not very pleasing," he said.
"To come to Scunthorpe and produce a gutsy performance like this is just what we needed."