India were without their premier all-rounder Hardik Pandya and his replacement Nitish Kumar Reddy also missed the tour of England with a quadriceps injury. Seamer Harshit Rana and all-rounder Washington Sundar also picked up injuries at different stages of the tour while pace spearhead Jasprit Bumrah missed Sunday's decider, which England won by 26 runs to seal a 2-1 series victory.
"If you look at the first squad, we had announced (for the series), from that minimum five players did not play this match," Gill said after their loss at Lord's.
"If one player is injured, you look at playing another combination, two players are injured you look at playing another combination, but if after every match some player is missing then somewhere we are missing a trick.
"If you keep the World Cup as the goal where we have to play 11 matches in a row, here we have players not being able to finish a two-to-three-match series.
"So there is some limitation where our players are not being able to play continuously, they play one or two matches, they suffer a niggle and then we are forced to play a different combination which we originally did not plan to play ... as a group we need improve our fitness."
England racked up 387-3 against India's depleted attack, while the tourists managed 360-7 in reply.
"Our bowling is a little bit inexperienced," Gill said.
"We were put under the pump in this match and we didn't respond well. We didn't start well in the powerplay. We gave away too many loose balls and then were always chasing the game trying to take wickets, create something which didn't happen for us."