I put some leftovers in the freezer last night (it was food that was in the fridge that I portioned out into baggies) and stacked on top of each other.The baggies in the middle still aren't completely frozen yet. Are they safe?
You say they started in the fridge, then you put them in the freezer, which is colder. If it would have been safe in the fridge, it will be safe in the freezer. So unless they had been hanging around in the fridge for a long time, they will be fine. Only you know what these bags of food were, and how long they'd been in the fridge, but most leftovers keep for several days in the fridge (rice is an exception according to some guidelines). Bought foods should have a use by date, and this is increasingly being described as use or freeze by (with the assumption that they'll be eaten just after defrosting.
In the future, try to disperse the food to be frozen. Your freezer may have a fast freeze button and shelf, which you can use in this case.