So I stole some bows and food from Flecher's shop in Solitude.

He didn't see me at all, I was using invisibility to move around and steal different items.

After I was done I sold some things to him.

I leave and wait 48 hours for his shop to restock.

When I come back in I was greeted with 3 hired thugs leaning on the front desk (where Flecher is) like they own the place.

I see Flecher sitting in the chair in back of them.

As soon as I got close they went crazy lol.

Weird that he didn't see me steal a single thing from him, yet he hired thugs to kill me...

It happens quite often that NPCs send Hired Thugs after you while they never saw you commit the crime.

Weird that they would be waiting for you in the same shop you stole from though.

Yeah they were leaning on the front desk like the owner of a shop would.

Note to self: Don't steal some thing and go back to the same shop a few days later.

Well, who the hell else was in the shop when everything disappeared?

I dunno about you, but I'd think the stranger that walked into town, snuck into an alcove, and came back out a few minutes later, with everything that was in the alcove in his bags, would be pretty suspicious.

True. And the CCTV probably helped too...

Well, it can't be anyone else BUT you from a meta perspective.

Although from a meta meta perspective killing his only customer is a really bad idea.

http://www.parks.ca.gov/?page_id=22319 are not evident on the in-game items but it could be implied that a crafter knows his own products.

Fletcher: "Sonofa....! Time to teach that thief some manners."

You can't sell stolen goods to normal vendors without perks. He probably sold other stuff, which was clearly enough to give away that he was in the shop at the time the stuff was stolen.

Sometimes they manage to hire thugs while dead.

Crime in Skyrim is really wonky. It made playing an assassin kind of silly. You kill someone in direct view of everyone, the guards come, and you pay your 1000 gold to get out of it. 1000 gold is nothing in this game. You can repeat this adnauseum without stiffer penalty. It's fun playing an assassin, but the penalties for being a bad one are tiny.

I murdered Sven and his mother. A week later I got attacked by goons hired by his mother, who was dead.

The reward is also only 1200, so if you are paying that 1000 gold, you are doing it wrong.

"That guy just became invisible and now all my stuff is vanishing... I didint SEE him do it so it cant POSSIBLY be him."

Another thing, if something has the "Stolen" property, it would be best not to sell it.

I had the same happen with good ol' Farengar. I quickly dispatched the thugs, then as I approached him he told me how much he values my friendship and gave me gold.

Ghosts are a well-established element of the Elder Scrolls universe. Often, the spirits hang around until some unfinished business is dealt with... like, say, their own murder.

Maybe it's a matter of time. Sending a letter to thugs, then said thugs tracking you down takes time. You just got to him before they got to you