Gillingham boss Martin Allen was disappointed to come away empty handed after Colchester won 1-0 through a late strike.
Substitute Andrew Bond scored the only goal to settle the contest after collecting a pass from fellow replacement Drey Wright as the Gills suffered a losing start on their return to League One.
Allen said: "I'm not sure we deserved to lose. Our lads need a bit of help so they can believe in themselves and win games at this level.
"We lost a key player after four minutes. Matt Fish had a fantastic season last year - it's his knee and he'll have a scan on Monday.
"What a game for young Stephen Butcher to make his debut - I'm really proud of him."