Injuries add to Newcastle United woes in Dortmund Champions League loss
Defeat means Newcastle face a fight to progress from Group F although they are still well-placed with four points from three games, the same as Dortmund.
But of even more concern to Howe were injuries to forwards Alexander Isak and Jacob Murphy.
Sweden's Isak lasted only 15 minutes before he was replaced by Callum Wilson, and later Murphy only lasted a few minutes as a substitute before falling awkwardly on his shoulder.
With games coming thick and fast, Howe said his squad could become stretched.
"Isak going off was a blow and Jacob came off with what looks like a serious injury," Howe said.
"We've got a small squad as is it. That's probably the most disappointing thing of the night.
"It looks like a recurrence of his (Isak's) groin problem and it's a big blow. Jacob looks serious, potentially a dislocation of his shoulder."
Howe also confirmed that midfielder Elliot Anderson missed the game because of injury.
"He's got a back problem so I think he's going to be missing a number of weeks," he said.
Newcastle face Wolverhampton Wanderers away in the Premier League on Saturday.