i feel like believing something exists is not problematic, however, expecting things is. prayer as i understand it shouldn't come with expectations. possibly requests but the deity provides as he/she/whatever sees fit. however with magical thinking, wishes are granted, etc. also, perhaps becoming so engrossed in magical thought that reality takes a backseat is the problem. many are engrossed in religion but it does not negatively affect their perception of reality.
not sure if this makes any sense at all, cold medicine makes creating complete thoughts a bit of a challenge
also, i very much agree with NinjaFrodo. believing in magical thinking is sort of lying to yourself, denying your logic