No, it is a problem when it is not consistent with first principles.
You do realize that out of some 26.4 million DNA sequences there are just 1098 known conserved non-coding sequences between men & mice and merely 32 versus non-mammalian vertebrates? Does it not seem quite plausible that random mutation may over the span of however long the lines of man & amphibian diverged managed to randomly conserve 0.000121% of the sequences? Or 0.00416% of the mouse sequences?
Well, that's just one possibility, and that's not even considering the likelihood of some underlying, undiscovered biological function that has lead to their conservation. The scientists have proposed several, and they will be tested in time. Whatever the case, I just wanted to point out that we're not talking about vast tracts of non-protein coding "junk" DNA here..
So here we have proof that huge chunks of DNA are completely unnecessary. So much for being irreducible. So much for showing intelligence in design. I have some of your (now banned) compatriots on record as saying there is no such thing as junk DNA. That is a failed prediction.
To the best of my knowledge, no mainstream biologist is on record as saying that because mutations can occur, they must. The question of why conservation occurs will be settled in the laboratory, someday.
Oh, I should mention that those figures may be somewhat out-of-date, though probably not by too much (unless there's been some major discovery I've managed to miss).