There's a couple issues here.... all of the rebar should be encased in a minimum of 3 in of concrete above and below. Since yours is at the surface it is not providing the structural the structural reinforcement that it was designed to provide. That tells me that your shell is either not thick enough, the rebar was placed too close to the surface, or the hole was not dug deep enough.
Placing mortar over the rebar won't do anything structurally and will just mask an issue that will surface at a later date. It is very common for rust stains to work their way up through the plaster and cause a huge discoloration. Every time this happens it is a result of rebar being too close to the surface.
The first thing I would do is drill a core sample in the shell and make sure that you have the full thickness that you need. If that's not the case then they need to come back and apply two to three more inches on top of what you have now to encapsulate the rebar. If by chance those are just stray pieces of rebar that are out of place then cover them up but then coat the entire shell with a high quality waterproofing agent like BaseCrete.
You're going to need to be your own advocate on this because the Builder is just going to want to do a quick fix and move on down the road. This issue will surface itself at some time sooner or later.
Good luck.... sorry that this probably isn't what you wanted to hear