Toyota Repair: A/T Oil Temp, fluid exchange, toyota 4 runner

Question
We just had the transmission flushed about 2 months ago.  Do you think they did something when they flushed it, like put in the wrong fluid?  -------------------------
Followup To
Question -
When we drive our Toyota 4 Runner 4x4 for an hour or more, the A/T Oil Temp light comes on.  After we stop and shut off the truck, the light goes off and turns on again after about an hour.  Can you tell me if there is a problem or what the light means?  

Also, we had the brake pads on the same truck replaced about 9 months ago.  Recently when we applied the brakes the truck would start to shake severly.  We took it in for repairs and the repair shop said we needed new brake pads, the ones we had were glazed over already.  We don't put on that many miles.  Can you tell me why this would be happening?
Answer -
The AT temp light problem can be solved by completely flushing the transmission fluid with a fluid exchange machine, find a toyota dealer or any shop that has the equipment to do this and make sure the correct ATF fluid is put in, it should be Dextron Mercon III, I had the same problem with my 4-Runner and doing this solved it.
The reason for the brake vibration may be because the brake disks are worn below the minimum thickness and are overheating under normal braking and warping, it is important that you have the brake disks measured to see if they are serviceable, if they are above the minimum thickness by at least 1mm they can be resurfaced on a brake machine,if it is less or near the limit the brake disk needs to be replaced, I recommend using the factory OEM brake pads and make sure all the anti-squeek shims and and anti-rattle springs are installed, just replacing the brake pads will not solve the brake vibration issue.

Answer
Yes. it is entirely possible that the wrong fluid was put in, most transmission fluids are compatible.
The temp light is turnred on mainly because the fluid starts to foam at higher temperatures and the temp sensor will pick this up as an overheating transmission because the foam and resulting fumes are hotter than the actual fluid. Try draining the fluid and replace it with
Dextron II or even better Dextron Mercon specification and see if it helps, the only other solution may be to install an auxillary transmission cooler.