Had a Quick look, couldn't find it in the top 5 pages or so I thought someone would have run into this by now.

To Replicate:
Pick any spellcaster. I used Lux when I encountered the bug.
Buy two tears.
Upgrade One to archangels, cast for a while and observe.
Upgrade the other to manamune, hit some minions, and observe.
Upon reaching the mana upgrade cap observe.

Observations:
Even though the archangels and tear have separate bonus mana increase rates, the tear maintained bonus mana level with the archangels, increasing by 5 each time a spell was cast.

Occassionally, there was a small window where it would increase only by 4 then update to be the same as that on the archangels.

Similarly, when the bonus mana increase for manamune was proc'd by the auto attack, a corresponding increase was seen on the Archangels.

Finally, upon reaching the mana cap, only one of the items would reach its promoted form, and the other would have its mana pool cap reset to 0.

Expected Behaviour:
Archangels and Manamune should have their bonus mana increase independently. That is, we should never have a situation where manamune's pool increases by 5, tears pool increases by 5, or Archangels by 4. The mana pool should also not reset upon completion of one of the items.

Guess as to why
the bonus mana pool appears to exist only once, and is depleted to create the upgrade. Most likely relic behaviour from when the mana increase for manamune, tear, and archangels were all the same in terms of updating the mana pool, and guessing coded behaviour for creating the upgrade.

Addendum
I haven't checked what happens with two simultaneous archangels (either created at the same or different times prior to upgrade), but that might want to be checked too. Unsure as to what to expect of manamune, but it may also experience the only one upgrades issue

The thing with that is that the passive is Unique. That's the reason why they share the same pool. Evolving independently would imply that both item will provide additional mana. I agree with you on some points, they could display it differently so we are less confused but other than that, that's the best explanation I can give you for this issue.