I recently started using a fluid drive trainer, the problem I've been having is, i keep getting flat tires on the rear tire, I never have problems like this when I'm on the streets with this same bike, i've have also checked for something puncturing the tire , but I have found nothing, could this be a heat problem ? i've notice the rear tire get very warm when I'm using the trainer.

You probably have way too much tension of the roller. Inflate your tires to the maximum rated pressure, then only apply enough roller pressure so the tire doesn't slip when riding. Do this trial and error keeping the pressure loose and listening for the squeal of slippage, bring up the tension by degrees until there's little or no slippage.

If all is right the trainer's roller should be in less than 1/8" or so from where it first touches the tire. If you bring it in more the excess flexing of the tire will be destructive to the tire causing overheating and tread separation.

If you have trouble with slippage with reasonable tension, try cleaning the roller with alcohol, or naphtha. If it still slips, you can treat the roller with spray adhesive, or do what I do. I use superfine glue on sandpaper to cover the roller. That allows great traction at almost zero roller pressure.