Problems mounting for Wigan Athletic boss
Latics were well beaten at Deepdale for the second season in a row, the visitors being flattered if anything by the 3-0 scoreline.
Stand-in skipper Danny Fox limped off just after the hour mark, with Joe Garner having to quit the action midway through the first half after a bang to the head.
And Cook revealed after the game substitute Joe Gelhardt was cut down before the action even got under way.
"Young Joffy did his hamstring in the warm-up, which was a bit of blow," Cook told the Wigan Post.
"He was going to play on Tuesday (against Stoke in the Carabao Cup), and we'll have to see how he is.
"Danny also picked up a knock and had to come off the field.
"The good news is Sammy Morsy's back training after a hamstring problem, and he'll be back in the side soon.
"Joe Williams is now over his injury, and that'll make us more competitive in the middle."
Cook readily admits there will be wholesale changes for the visit of the Potters.
That could mean first starts for new signings Williams, Jamal Lowe, Kieffer Moore and Charlie Mulgrew.
"You know me, there'll be changes, and plenty of opportunity to change the side," Cook added.
"The Carabao Cup, in terms of our priorities, is our least one.
"Our bread and butter is the league, the FA Cup would be second, and the Carabao Cup third."
Cook also hit out at referee Jeremy Simpson for the events which followed Garner taking a powerful shot from Ben Pearson right in the face, which led to him temporarily leaving the field before coming back on.
"There was nothing wrong with Joe," fumed Cook.
"The referee was saying Joe was unresponsive when he was down, but Joe is saying he was telling the referee he was fine.
"That gives us a little bit of a problem, when the referee is saying he's unresponsive and Joe's saying he's fine.
"The ball's obviously gone out for a corner, Joe should never have left the field, and from the corner they score the first goal.
"And this is one of the things that managers are getting disgruntled about.
"Joe Garner's one of our markers at corners, it's left us a marker light, they go and score...is that correct?
"Having said that, the referee hasn't cost us the game, let's have it right."