Well, you have a seam there and it's going to be hard to get the patch to seal around that seam. If I'm looking at this photo right. I think you *might* be looking at getting another liner. Teald024's advice is good. But, with that seam, it's going to be hard. And, I think you're going to want to drain it to get into and work that seam. You'd need an oxygen tank to be able to stay down long enough to work it. Once you have it patched or replaced, you're going to want to prevent this from happening again and I think your pump might be a bit too strong for the cleaner, so if you have the plunger valves, use these adjust the flow and slow down the cleaner. It should not be hitting the side of the pool that hard. This is why the hose connections leak on that cleaner, to take some of the pressure out to prevent it from slamming into the sides with the higher powered pumps. If you've tried to resolve these leaks thinking they were bad connections, unresolve them. They're there for a reason. Otherwise, use the plunger valves to reduce water flow. I've had mine for 3 years and have never had an issue with it putting holes in my liners.
I'm also thinking that your original Intex liner is off center from the looks of the photo. It's kind of hard to tell from the pic, but I think that's what I'm seeing. That drain hole should be more up on the side rather than kind of half on the bottom and half on the side. That's going to make it jut out into the pool more than it's intended to. I shouldn't be pointing directly at the ground on the outside, it should be parallel to the ground. If I'm correct on what I'm seeing, you're going to have to readjust that outer liner correctly, which also means draining the pool.
You sure it's the wheels and not the outflows on the cleaner? Those would hit the side before the wheels would and stop the wheels from ever contacting the side of the liner. If it's the wheels, then the cleaner is coming up the sides a bit and adds to my suspicion that your flow is too much for the cleaner. If you find that it's the outflows rather than the wheels, you could try some "Flextape" to cushion the edges. OR, you could just try using the Flex Tape to seal the leaks AND it would add cushioning protection to those areas as a bonus. The seam is still going to be an issue, but it might work better than pool patch. But, I still recommend reducing the flow to the cleaner either way. It really should not be hitting hard enough to put a hole in the liner. That's the dead give away that it's getting too much water pressure. You'll need to reduce that somehow.
Whatever you end up doing to patch, I think you're going to want to patch from both inside the liner and the outside.
I'm also thinking that your original Intex liner is off center from the looks of the photo. It's kind of hard to tell from the pic, but I think that's what I'm seeing. That drain hole should be more up on the side rather than kind of half on the bottom and half on the side. That's going to make it jut out into the pool more than it's intended to. I shouldn't be pointing directly at the ground on the outside, it should be parallel to the ground. If I'm correct on what I'm seeing, you're going to have to readjust that outer liner correctly, which also means draining the pool.
You sure it's the wheels and not the outflows on the cleaner? Those would hit the side before the wheels would and stop the wheels from ever contacting the side of the liner. If it's the wheels, then the cleaner is coming up the sides a bit and adds to my suspicion that your flow is too much for the cleaner. If you find that it's the outflows rather than the wheels, you could try some "Flextape" to cushion the edges. OR, you could just try using the Flex Tape to seal the leaks AND it would add cushioning protection to those areas as a bonus. The seam is still going to be an issue, but it might work better than pool patch. But, I still recommend reducing the flow to the cleaner either way. It really should not be hitting hard enough to put a hole in the liner. That's the dead give away that it's getting too much water pressure. You'll need to reduce that somehow.
Whatever you end up doing to patch, I think you're going to want to patch from both inside the liner and the outside.