I have a Shimano BR-MT201 Hydraulic Disc Brake on my rear brake. I was replacing the brake pads and accidentally pressed the brake too many times and the piston popped out leaking brake fluid. Afterwards I pushed the pistons back in, retracted them all the way and pumped new brake fluid into my brake. But now, when I press the brake the pistons don't move at all and the brake easily compresses all of the way. I also noticed a little air bubble around the piston when I press the brake. What should I do to fix this? I have also cleaned the piston with isopropyl alcohol.
From your description, it seems that either there are air bubbles in the brake lines, or the cylinder assembly lost compression. What can - or should - be done about it, depends largely on the extent of the damage caused by the popped cylinder.
If you are lucky, proper bleeding should do the trick. However, the bubble of air forming near the piston suggests there is more to that. If the piston picked up dirt from the floor and you pushed it in, it's possible that the seal, piston, or the entire cylinder got damaged. A grain of sand could also explain why the piston is not moving at all.
You can try bleeding the brake according to the manual, but if that doesn't help, replace the pistons (if you could find them, Shimano does not list this item in the manual). Keep in mind, though, that Shimano hydraulic brakes use mineral oil as working fluid, not automotive DOT fluid. Using DOT 4 (the most widely used brake fluid) can irreversibly damage seals and hoses.
Here is the link to Shimano's Dealer Manual for BR-MT200. There are a couple notable lines in the beginning cautions and recommendations. One states that if a piston were to completely come out, "consult a bicycle service center." The other, "Do not remove the pistons when disassembling the calipers (for cleaning)." This manual also has the proper bleed procedure laid out which should be followed. When doing this, note the caliper should be at the low point. Remove it from the bike or fork so that one, the hose is a fairly straight shot up to the lever, and two, you can turn and tap the caliper to better get the air bubbles moved out of the caliper.
The pistons are held in place by the force of the rubber seals. The edge of the rubber seal will rest in a seat on the piston and form an air and oil tight seal. In addition to the sealing effect, the stretching of the rubber seals when the piston moves in toward the rotor creates the force that returns the piston back to it's "at rest" point a millimeter or so away from it's side of the rotor. So, when you state, "the piston popped out leaking brake fluid," that infers the seal of the rubber to the piston was broken (not necessarily as in damaged but displaced from it's seat). You go on to describe pushing the piston back in. I wonder if the seal has not been seated properly on the piston allowing air in or not allowing appropriate pressure to build behind the piston upon lever actuation.
The fact that the pistons are not now moving indicates a situation where there is inadequate pressure build up to move the pistons. This could be air, which is compressible and any within the system steals the hydraulic pressure the fluid exerts, or an incompetent seal (damaged, unseated, or foreign object between seal and piston). There could also be a slight misalignment or something that causing a mechanical blockage that prevents piston movement even under normal hydraulic pressure build up.
I suggest determining what the issue is by examining the caliper and it's piston area while actuating the lever. Is there any pressure build up? Determined by lever feel. Is it soft initially? Does it firm up any with multiple lever actuations? Do you hear or see anything at the caliper? Air or oil leak or both? Feel anything at the caliper like vibrations or the movement of fluid or a sensation of air bubbles squishing through fluid?
Obviously we need to determine adequate piston to seal integrity but that will be tough to do if you can't get the retracted pistons to move out. A continued soft lever feel under multiple actuations and in the absence of any signs of leak (sight, sound, feel) is better evidence that there is air in the system. At any rate, if the pistons aren't moving at this point--if nothing is happening, like leaks--complete a proper bleed by following the "adding oil and bleeding air" section of the above dealers manual. Have the caliper off the bike and hose straight up to the lever which is parallel to the ground (you want the port that accepts the funnel to be the high point of the system which is naturally achieved by it's design if it's positioned like was sitting on a table. The installed funnel will be pretty much straight up and down, the top of the mineral oil in it forms a level, horizontal line). When adding the mineral oil with the syringe, move the caliper in different positions keeping pressure on the syringe so oil continues to flow. Use your other hand (or a helper) to tap the caliper and hose with the handle of a screw driver. Vary your pressure on the syringe a few times, soft then firm. Always keep a little positive pressure or you can stop completely but don't suck the plunger back. All of this helps to get air moving out of the caliper. Obviously, a leak or bubbling anywhere as you do this needs to be evaluated. Both the syringe and funnel need to be connected air tight. There should be an o-ring for the funnel and the plastic tubing off the syringe should fit tightly on both syringe and bleed nipple.
At #5 of the bleed procedure in the dealer manual where the syringe is replaced with a collection bag, note the upright position of the bleed nipple and initial aspect of hose. Keep these in a generally up position as you manipulate and tap the caliper body and brake hose.
With bleed complete, check for piston movement and leaks etc. One thing to note, the BR-MT200 is a fairly inexpensive item. A whole new system for front or back brake can be had for $25-40 USD. That's pre-bled, one can install and go pretty much. Thus, if your time is more valuable than your willingness to jack around with all this perhaps it's best to buy new and have a spare lever and a caliper to dissect for understanding. Here's one link of several options for ordering a new BR/BL-MT200 set, chosen for the sale price and multiple positive experiences with the seller. Call that what you want except a "recommendation" which is frowned upon here on SE. Universal Cycles. Sale on BR/BL-MT200 and others