Flooring Tile - patching underneath

I have a house poured on a concrete slab. I am tearing out the old ugly tile in the bathroom. In a few places where the nails where to hold down the carpet the concrete is coming up and leaving small craters basically to describe it. Is there any type of material or substance to use to fill in the small holes so i can lay new tile down. I am laying the tile that just sticks to the floor and i'm worried if i don't fill in the holes down the road it will cause problems, and since i'm starting from scratch I thought I better do it right the first time. Any suggestions would be great. Any other suggestions or tips on installing this type of tile would be great as well. Like should I use anything in between the seams of tile. to make sure they seal since it is a bathroom?

i use ardex feather finish for that type of problem,works great.
The issues that will arise when using this kind of tile are that the tile tend to shrink when placed on a cold concrete floor,and they generally don't stick very well.
If ceramic is not an option then fil in all holes and and scrape the floor to make smooth,also make sure there is no oil, grease, wax,dust or anything that will hinder the application of the tile.Get some thin spread adeasive and a 1/32 notch trowel.Snap a control line on the floor to keep you straight and lay the tile:cool:

I was talking with someone about it and they suggested that i might save the work and just take up the tile where it's come up and seal it and level it then put down a sub floor over the old tile. would that work for me or against me?

Adding a subfloor over a slab is a no-no. Remove the existing floorcovering and all its hardware and patch the floor with Ardex feather finish. The Ardex is easy to work with. Mix it a little thicker than drywall compound and spread it onto the problem areas with a six inch taping knife.