Rovers suffered their first defeat of the Butler era with a 56th-minute goal from Mikael Mandron proving decisive as the Railwaymen secured a league double over Doncaster and extended their unbeaten home run to 11 matches in League One.
It was a night when Rovers played without a recognised striker with Omar Bogle and Fejiri Okenabirhie missing through injury, with matters compounded by Reece James and John Bostock coming off with problems in the second half.
Butler commented: "Reece has taken a knock to the calf and John had a little bit of a groin twinge. With John, it is a no-brainer to bring him off if he's a slight injury and it is the same with Reece with an impact injury.
"Omar felt his hamstring after Saturday's game and we have just to manage his work-load. He has played a lot of football in the last four games, compared with not playing for quite a few months and with a hamstring injury, you have to be careful.
"We are going to have a look at him and Fay(Okenabirhie). Hopefully, they will both be in contention (for the weekend)."
On his side's display, he added: "The endeavour was there, but we just lacked the final killer pass and final third entries.
"You look at what they (Bogle and Okenabirhie) bring to the side and the threat that they carry and it is never easy when you are without a recognised striker on the pitch, although Madger (Gomes) did a job. But we never really threatened them and they were comfortable in the end.
"Madger has played high up before and so has Taylor Richards, so we allowed them to switch along with Copps (James Coppinger). I thought they out of possession,they threatened really well. It was just the final pass tonight.
"My feelings at half time were that we caused our own problems. But Crewe is a tough place to come and they are 11 unbeaten now at home and I cannot fault the players desire and I thought we grew into it in the final ten minutes."
Butler, whose side saw an early goal disallowed after Jason Lokilo's strike from a corner was ruled out for a foul on keeper Dave Richards, Butler said: "The corner went in, in the first half and the referee spotted a foul, which we had not really seen and five minutes later, our keeper got clattered and nothing was given and that was disappointing from our point of view."