Hi PicachuForever,
Thank you for taking the time to report this and I apologize for any inconvenience you may have experienced. After several attempts by multiple people to replicate this bug, it is believed that what you experienced was a visual bug. In all of our trials, despite the hydration message not appearing at the end of the original turn, in the successive turn manaphy was able to act as well as be statused by the opposing pokemon. This indicates that manaphy did wake up after being swapped in under the rain.
If this is not what occurred for you (i.e. you specifically remember your manaphy being unable to act in the next turn), please assist us by listing as many steps leading up to the event as you can remember.
Again, thank you so much for bringing this to our attention. Have a wonderful day!