Gill was speaking after India suffered a 27-run defeat in the deciding ODI against England at Lord's on Sunday as the visitors fell to a 2-1 series loss.
The tourists missed the services of fast bowler Jasprit Bumrah for the contest while Washington Sundar, Harshit Rana and Nitish Kumar Reddy were also injured.
Gill said: "If you look at the first squad we had announced [for the England ODI series], from that minimum five players did not play this match.
"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 and 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.
"So keeping all this mind it becomes a little difficult that you come to the ground on the morning and you come to know a player has a niggle, then it's almost like do you want to take a chance?
"Some player is 80% fit, you are playing with five bowlers and if this player comes out after bowling five overs, then who will bowl? This is difficult. So as a group we need improved our fitness and all those things."