Those gaps should be sealed. Is he coming back? Have you paid for the job?

+1. You typically trim that out with site formed coil. They should be foamed as well.

+1. Looks like an incomplete job. Where was this left off in terms of communication on the status?

He said he will seal them with mortar later as he does not have the crew to do it now. He is working on interior paint now. But my concern is that this has been left like this for almost 2 months not. Shouldn’t we be concerned about water getting in from those gaps and cause mold issue?

Mortar is wrong in this application if you ask me. As HomeSealled Exteriors said, brick is water shedding and not waterproof.

Your contractor didn't pay enough attention to the depth of the jambs on your original windows and ordered new windows with a narrower jamb. Filling that gap with mortar isn't a real solution. He'll probably have to add some type of molding around the perimeter (vinyl, wood or aluminum).

The attached photo is not one of our jobs.

Thank you so much everyone for your helpful comments. Is aluminum molding something that can be added now?

Normally a window company would have nothing to do with mortar, a mason would need to be hired by the homeowner.

Aluminum trim can be added as this point. This, i.e. after the installation but not 6 months after, would be when it is normally installed.