Adding the acid after mashing in isn't a big deal, but you should recognize that there can be problems. The first problem is that the water's alkalinity will drop a bit as its heated. If you start with low alkalinity in the first place, this heating effect is of no concern. If your water has a bunch of alkalinity, then you might end up overdosing the water with acid.
The second concern with adding acid in the mash is getting it mixed in and fully distributed. Tests have shown that it is very difficult to mix a mash very well...even with Herculean effort. However, if you run one of those recirculating mashing systems like HERMS or RIMS, then the acid will get distributed in a few minutes of recirculation. For most brewers, adding all the minerals and acid to the water before adding the grain is the surest way to assure that those components are fully distributed in the water.