The Addicks lost 2-0 at The Valley to bow out of the competition. Next up are crunch League One fixtures at Blackpool on Saturday and then league leaders Portsmouth next midweek.
And Bowyer says Tariqe Fosu, Krystian Bielik and Karlan Grant all reported with niggles on Thursday.
Bowyer said: “Tariqe didn’t train Thursday because his groin had tightened from Tuesday.
“Krystian was meant to play in the game but on Thursday he walked in with a tight hamstring from Tuesday – and so did Karlan.
“So three players who we used on Tuesday couldn’t train. You think: ‘Wow, I can’t risk anyone else if they are struggling’. Even Joe Aribo was still sore from the Burton game – and he’s a machine.”
Bowyer made nine changes for the Doncaster tie and believes it was still productive in terms of gauging where some of his other players are at.
“I learned that [Ben] Reeves is further off than I thought he would be. He looked sluggish to to me. He looked a little more off it then I’d have liked. He does well for us Reevesy, he is that clever one in the middle of the park.
“He looked a little off it but he might improve this week in training. We’ve got a full week to prepare for the game.
“Billy Clarke looked better than he has done in other games but is he ready yet? Probably not. But he’s getting better – that was a plus for me.
“I think it was the right decision to make changes. Our squad isn’t big – that speaks for itself – and it would be silly to risk anyone.
“I respect the cup but it’s different for sides who have big squads. Even if I didn’t have so many injuries it would be different, all of ours have come at once and they are all eight, 10 or 12 weeks.
“We only lost to two set=plays. The young lads handled themselves okay. They had a bit more pressure than us but we created chances, enough chances to win on another day.
“I’m disappointed at the result but it was quite successful for me in terms of asking could I trust them to play on a Tuesday night? We had got a lot of Saturday-Tuesday games coming up.
“We could’ve picked up an injury. Don’t get me wrong, we could pick one up in training tomorrow – I understand that. But at least we’re a bit more in control of that.
“On Saturday you could have a centre-half who is not happy because Lyle Taylor is dominating him and he comes through the back and he is out for six weeks – in a competition which we are never going to win. There is no point in that.
“I’m not gaining anything and I’m losing Lyle for six weeks, our top-scorer.
“I’m looking at the bigger picture, some people might not like that. But my job is to get promotion – not to win that cup.”