My son (my qualified dependent) filed his taxes this year and did not mark the box that states someone else can claim me on their taxes, will this delay my return?

Yes, you will likely need to file your return by mail as he will need to amend his return to indicate that he can be claimed as a dependent on someone else's return.  If his return is rejected then he can change that error on his return then, and you can e-file as usual.  

If his return is accepted:
He will need to amend his return, once it has been accepted and any refund due has been paid out.  Then, he will go back into his return (following the amend instructions) and find his name in the Personal Info section. Click to edit beside his name. On the following screen near the bottom, he will find the area to click that he can be claimed as a dependent by someone else. I will attach a screenshot of that area, so you are better able to locate it.