Tony Pulis admitted it was disappointing to concede goals at the end of each half following the 2-1 defeat to Chelsea.
Abdoulaye Faye headed Stoke City ahead after 32 minutes at the Britannia Stadium but Didier Drogba then equalised for Chelsea during an eight-minute period of injury time at the end of the first half.
Stoke had already lost James Beattie and goalkeeper Thomas Sorensen to injury by this point, leaving Pulis with just one more available substitution for the rest of the match.
The Potters battled hard for the rest of the match but suffered an agonising defeat when Florent Malouda struck in the 94th minute.
Pulis told Sky Sports: "It is disappointing.
"We have given it our best but unfortunately we picked up a couple of injuries and when Chelsea were coming on strong in the second half we were unable to bring on Ricardo Fuller and Matthew Etherington.
"Both (goals came) in injury time which was disappointing but irrespective of what time he (the referee) puts on, you have to defend properly."
Stoke had to withstand long periods of intense Chelsea pressure but they did carve out a couple of good opportunities themselves.
Pulis said: "Beattie missed a good chance in the first half and Dave Kitson had a great header that on another day he scores, but you are playing against one of the best teams in Europe."