How do i change the rear brake pads on a yamaha xt 250

Your pads are probably shot. Replace them.

Yes, it has rear Disc Brakes, I would suggest to change the rear pads since they have to remove the rear Brake Calipers to remove the rotors and it wouldn't take much more time or labor to replace the pads at that point. That way when your rear rotors are re-installed and your new brake pads are installed your rear brakes should give you longer service life and better stopping power.

Rear disc brake pads offer better performance and are not as affected by moisture like conventional brake shoe style brakes are. Rear disc brakes are similar to front disc brakes. The main difference is that rear disc brake systems must incorporate the emergency brake system. There are two methods widely used for the emergency brake with rear disc systems. The first system is a brake shoe inside the brake disc that is actuated by the emergency brake lever. The second is a screw style actuator inside the brake caliper. When activated the brake pads are forced into the brake disc and held tightly by the emergency brake lever.
READ COMPLETELY BEFORE STARTING
Step 1 - Identify Rear Disc Brake Components
Rear disc brake assembly includes; rear brake disc, rear brake pads, brake caliper mount and a caliper mounting screw. (Note: Some vehicles do not have the rotor mounting screw.)
Step 2 - Removing the Rear Brake Caliper Mount Bolts
To replace rear brake pads and rotors the rear brake caliper needs to be removed. First loosen the rear brake caliper mount bolts and remove them. Turn counter clockwise.
Step 3 - Lift Rear Brake Caliper from The Caliper Mount
After the caliper mount bolts have been removed, gently lift the brake caliper from the caliper mount. Inspect the caliper slides; they should move freely in the caliper mount. Remove rear brake pads and hardware.

Step 4 - Removing Caliper Mount Bolts
With a socket wrench or other appropriate removal tool, loosen the rear brake caliper mounting bolts. Remove bolts and lift the caliper mount and remove it from the vehicle. Remove the retaining screw from the disc mounting hole. Tap the rotor gently to release any rust that has accumulated between the rotor and bearing hub. Lift brake rotor from wheel hub holding on tightly, using both hands. You do not want to drop the rotor.

Step 5 - Removing Rear Brake Rotor
Remove the retaining screw from the disc mounting hole, tap the rotor gently to release any rust that has accumulated between the rotor and bearing hub. Lift brake rotor from wheel hub, hold on using both hands and do not drop.

Step 6 - Install New Brake Rotor
Check the new rotor against the old brake rotor to make sure they are the same size. Clean the mating surface on the wheel hub before the new brake rotor is installed. Reinstall rotor retainer screw.
Step 7 - Reset Rear Brake Caliper
Before new brake pads can be installed, the rear brake caliper must be reset. The reset tool winds the piston back into position so the new brake pads will fit. This style of brake caliper will not compress with a clamp tool; it can only be reset with the proper reset tool.
Step 8 - Reinstall Rear Caliper Mount and Install New Rear Brake Pads
After the caliper has been reset, reinstall caliper mounting bolts and make sure the bolts are tight. Then match up the old brake pads to the new brake pads. They should be exactly the same except, of course; the old ones will be worn out. Check the new brake pads for proper fit and install any brake hardware that is required.
Step 9 - Remount Rear Brake Caliper
Reinstall the brake caliper, align brake pad hardware and reinstall caliper mounting bolts. (Note: align the rear peg of the brake pad to the groove in the caliper piston.) Recheck and retighten all caliper and caliper mount bolts. Bleed brake system to relieve any air in the system. Before driving the vehicle, push the brake pedal down and let it up slowly. This operation forces the brake pads to travel to the brake rotors. DO NOT DRIVE VEHICLE until proper brake pedal operation resumes. When test driving vehicle listen for any unusual noises during the operation of the brakes.
WARNING! Always have the vehicle under inspection on level ground, in park with the emergency brake on. Always wear protective eyewear, gloves and necessary clothing before inspection or work begins. Never crank an engine over when anyone is near the battery or engine. Always have an operational fire extinguisher close by, obey all first aid instructions in the event of an injury. Never stand in front or behind a vehicle when cranked over or running. When engine is cranked over keep hands and clothing away from rotating components. Never move a car without proper brake pedal operation.

That's to be expected and is completely normal.

Rear brake shoes as fitted to drum brakes can typically last up to 60k miles with periodic adjustments, but you have rear disc brakes and the shoes will typically last half of that.

Also, modern brake pads no longer contain asbestos and are now made using harder metallic compounds; the direct result is that brake discs (US=rotors) are also considered to be consumable items as they are worn down by the harder pads. It's not unusual to have to replace front discs every other pad change and rear ones with every pad change; in both cases the mileage will typically be around 30k miles on most models.

Whilst riding ,try pushing the brakes with the clutch in and if you still hear the noise it will most likely be your brake pads(possibly worn to metal) or the discs themselves.

Replacing stock or worn brake pads is the quickest way to get increased braking power out of a tired system. Various manufacturers make all kinds of different types of replacement brake pads for today's motorcycles. Some claim to last longer, while others claim to give more feel and braking power. However, be forewarned that the manufacturer of your motorcycle put a lot of time and effort into developing your braking system, and there is no telling what a different type of pad material might do to your rotors or how well different pads will work with the overall design and setup of your bike. If you have any doubts, then stick with genuine factory parts. Removing the calipers from the rotors is the first step in checking your brake pads. In dealing with your front disc brakes, first remove the Front Caliper two main bolts that attach the calipers to the forks. Once the calipers are free you can slide them off of the brake discs and inspect the amount of pad material and look for anything out of the ordinary. If there is less than 1/8 inches of pad thickness left then they should be replaced