How did the Reverse Flash beat up Harrison Wells?
The Harrison Wells in Season 1 was not really Harrison Wells at all. He was Eobard Thawne, the arch nemesis of the Flash from the future. As he himself described, he is everything the Flash is not, he is his antithesis, the Reverse Flash.
Apparently in the future, Thawne became Barry's arch nemesis. His hatred for Barry was so great that one day, he decided that he would go back and kill Barry when he still was a child so that he would never become The Flash, even though this would erase Eobard himself from existence. Now, as we know he failed, killing Barry's mother instead! Eobard Thawne was stranded, stranded in the past with no way to get back to the future! On top of that he lost his connection to the speed force since Barry no longer existed. I assume Thawne was unaware that Barry was THE speed force at that time. He came to the sinking realization that he had to create The Flash in order to get back. So as we all know, he took the place of Harrison Wells, and created S.T.A.R labs...creating the particle accelerator..triggering the explosion...leading us to where we are now; How did he beat himself up in that room?
First, Thawne knew that he could not let there any be clue that he himself was the Man in the Yellow Suit. He knew that Cisco had built the field such that he would not be able to get in or out once it was switched on. Now, if The Reverse Flash never showed up despite the bait of the tachyon device, Team Flash would start getting suspicious that one of their own was the Reverse Flash. No. No! He could not have that happening could he?
So he came up with a brilliant idea. With the future knowledge and the intelligence of Wells( I assume the DNA splicer took a bit of Well's personality and intelligence too) altering Cisco's code was a piece of cake for him. He decided that he would use a hologram to show him as RF entering the enclosure, program it to wait till they could come out, thus allowing him to be close enough to create a speed mirage( or time remnant?).
Again I assume that while they were hiding , Thawne was too far to create a speed mirage(time remnant), he had to get closer. So the moment they were close, the hologram ended, and he created a speed mirage, activated his failsafe, allowing him enough time for his speed mirage(time remnant?) to grab him and do a decent job of beating himself up to convince Team Flash.
Hope this answered your question.
P.S. You must have noticed the bit about the time remnant. Well, with developments of Season 2, I wonder if RF beating up Wells was a time remnant instead of a mirage since speed Submitmirages cannot exactly touch each other if I am correct.