Mesmer Mantra's
I seem to encounter a similar issue.
I have Harmonious Mantras traited, and when I charge up my mantras, I get my 3 charges. I don’t know what exactly causes it (it does not happen on downed like OP), but I very often randomly go from 3 charges to 2 charges on all my charged mantras. This makes the trait very unreliable and worthless.
I think it has something to do with entering and exiting combat, but I’m not sure yet. It only seems to happen after a few minutes of charging up the mantras. I’ll post more details if I ever figure it out, but this is definitely a bug and should be looked into.
It’s linked to transitioning to an area that has a different level scaling cap.
For instance, if I’m on my level 80 character and I’m in a zone that scales me down to level 4 (i.e. at the start of the plains of ashford), I can charge my mantras up to 3 uses and do this as normal.
However, if I have my mantras charged and I walk over towards the next area (i.e. heart quest) and it adjusts my level to 5, my mantra charges will all be reduced to 2 if they were at 3 before entering the area.
If I use up those 2 mantra charges in the level 5 zone and then recast the mantra, it will give me the 3 charges again. However, if I walk back to the level 4 zone, it’ll put any that are at 3 back down to 2.
I’m guessing the same thing is being observed by you two. Furthermore, I would predict this happens on any sort of level scaling transition, meaning it should happen quite frequently in PvE areas. However, I don’t think it should be happening it places like WvW, fractals, or dungeons. If you’re observing it there then there is likely a secondary cause for this.