Just bought a house. I have a second story tile shower. I noticed while showering that the tiles under my feet were squishy. I removed the floor tiles and there was standing water between the tile and concrete. It only took me 3 minutes to pull up floor tilw it was not set right. I looked through the drain line and I do have a pan under the concrete. Should I bust up concrete and replace the pan and relay the concrete or ahould I just retile properly and see if that works? Also there is an old ceiling stain under the shower on the first floor ceiling but has not been wet or grew since we moved in and used the shower daily for 4 months.

Since the ceiling below is now dry, I would just redo the tile. But you won't have use of the shower for a long time. Aim a fan at the concrete after cleaning it, for days, until totally dry, plus there's drying days after you tile.
To know if concrete is dry, duct tape heavy square of plastic down on it for 48 hours. If moisture collects under it, it's not dry. Concrete is porous. It may take quite a while.

There should never be standing water in a custom, " mud set ", tiled shower base. Standing water would indicate a problem with the shower drain weep holes, or the vinyl or rubber shower pan liner is not properly pre - pitched towards the drain...

Mike nailed it! If you have standing water when the weep holes are clogged. Remove the tile and mud a clear the weep holes . You may now proceed to install a new tile floor. Good luck, Tom

Yep, Speedball said it: clear weep holes and you are back in business... Back to you.. Milo