Yes it is a problem from a couple of POVs. First, assuming it was used because dough in pH was too low, it doesn't raise it fast enough to set pH within the desired range for the first set of enzymes (be they beta glucanases, proteases or amylases). But chalk is the gift that keeps giving. Over time more and more acid is neutralized and the pH continues to rise. Beta glucanase rest pH might be too low, saccharification pH or kettle pH may be too high. pH in the fermentor may be too high (i.e. high to the point that the yeast have establishing the pH they need.
As I have said many times before if one's mash pH is 5.0 or less something is wrong. Look to recipe, the means being used to measure pH etc to determine what it is. If you, with open eyes, use enough black malt or accidentally put in enough sauermalz to get the pH down to 5.0 or less then neutralize it with lime or sodium carbonate.