Paul Sturrock acknowledged it was not Southend's night after watching his side go down 1-0 at leaders Gillingham.
The visitors had goalkeeper Paul Smith stretchered off early on after a nasty collision with Gills striker Deon Burton, before Ryan Cresswell brought down Bradley Dack for a penalty just before half-time which Danny Kedwell converted.
Dack then quickly saw red for a lunge on Mark Phillips, who was forced off injured at the interval, but Southend could not make their numerical advantage count in the second half as Gillingham relied on some desperate defending.
Sturrock said: "We are disappointed. The referee's decision has been a feature of the game. We had a certain penalty denied.
"Coming here to a difficult place, they are the form team at the minute and we competed with them all night. Their goalie had more saves to make than ours. I was disappointed with our final ball, that final cross and that final finish which let us down a bit in the second half.
"I just felt that one or two of our players were off the pace compared to the weekend but we have to take the positives throughout the game. I didn't think we deserved to lose the game. The substitutions were dictated by injuries which didn't help things and we were chasing the game with our height and it just didn't seem to be our night."