So, I heard that you can use your follower as a mule by packing a bunch of stuff into a container and then telling your follower to take it. I tried this with Lydia while on a dungeon crawl, but when I took the items back while in town to sell them, all of them had been labeled stolen. They were not initially stolen, just stuff I had picked up in the dungeon. Is that normal? If so, how do I get around that?

Did you pack your stuff into a container that wasn't yours, or a "free" container?

It's best to tell them to pick something up individually, instead of all together.

I'm pretty sure it was one of those large urns you find in a draugr barrow. I had just looted it when I got the message that I was over burdened. So, I guess it was a free container.

Next time, I'll try one at a time, to see if that makes a difference. But there is little use in using a follower as a mule if each item must be swapped back and forth individually. That would take a burdensome amount of time, it seems to me.

Still, is there a way to make stolen items not stolen anymore? I know that is kind of a cheat, but in my opinion, these items weren't stolen to begin with.

You could always go to a TG fence.

This.

I'm not sure about a bunch of items but you can use the end table next to Farengars bed in Dragonsreach to clear stolen tags by telling followers to take the items out.

One way to get around this is to use the RP'ing rule to only carry what you could realistically carry. Once I adopted this rule, I stopped getting overburdened, and I usually weigh 30-60 pounds and my followers always have what they started out with, and maybe a little food or something but nothing more.

I'm still trying to figure out why all of his items became marked as stolen.

As noted in the bugs section http://www.uesp.net/wiki/Skyrim:Followers#Bugs :

Items may become flagged as stolen: If you place items in a container and then command the follower to "take all items" the items they take from the container may now carry the "Stolen" tag.

Ah Ha! I see... well I am glad I learned of this bug.

It's shame when there are so many bugs in Skyrim, you learn about a new one every week.

You would think in a game where we have horses as mounts, carriages to take us around, and find wagons attacked by bandits with trade goods that the game could have given us pack horses so we wouldnt have to make our own out of followers.

Thanks to everyone who responded (I will use the fence), but this ^^is really what I was after. Knowing it's a bug, makes it somehow easier to take.

Making followers go over their encumbrance limit by having them pick things up can lead to all sorts of bugs, including having the stolen flag set on everything they carry. Items have also been known to just disappear. This exploit is not recommended.