The glitch is the following:

 

You put some prayers (example: protect from melee, steel skin, ultimate strength, ...)

 

 

 

When you did this you open your emotes menu and click an emote you can't use yet. A chat box will appear saying what you need to do so you can use it ("this emote can be unlocked during the Lost Tribe quest", many others are possible)

 

 

 

Just don't close this message and watch your prayer now and you can see you aren't losing any prayer =)

 

 

 

 

 

When you are attacked this message will close so you can't use it while fighting. However, when (most members) you are dd and waiting for other clan/player you can use this so you don't need to turn on your prayers when you see them ..

This is an old one and is already recognized by JAGeX. It is not a glitch.