If you used the Intel bracket, then your cooler is not installed correctly. Yes, it is a problem. You should first verify that you do in fact have the wrong bracket, for sure, and if so, then remove the waterblock and bracket and clean all the thermal material from both the bottom of the water block and the top of the CPU with isopropyl alcohol and lint free cloths or paper coffee filters, and then apply fresh thermal paste (Which you will likely need to buy) then reinstall using the correct bracket.
I'm not even sure how you possible COULD install it with the wrong bracket, but if you did, somehow, it needs to be corrected.