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Status effect HUDs can at times persist when they should be hidden.
If multiple effects from different heroes that change max health are applied to a player at once it will not result in the right max health.
If your max health changes you may lose any health you had above your default max.
Temporary effects given by another player can last forever if that player leaves the game before the effect duration ends.
Any upgrade for a targeted ability such as Orb of Discord or Guardian Angel can target the wrong player if the closest player to the crosshair is not the targeted player by the ability. This can happen since the targeting diamond is slightly elastic and can stick on a player after the crosshair as moved for a moment.

Mercy
Combo Beam, Fortification Beam: Can be activated with pistol equipped.
Zombie Effect: If Resurrect is canceled, the targeted player will still get the buffs when he respawns.

Mei
Ice Launch: If ice wall is rotated so it projects perpendicularly you still have to look just as far down to get the launch to activate, so there are some instances where Mei pops up with the wall but is not launched.
Snowstorm: If Mei is affected by multiple damage buffs from vanilla Overwatch (Mercy damage beam and Ana nano boost, for example) while she throws blizzard, the Snowstorm upgrade will not take effect.

Pharah
Purify: Quick melee activates burning.
Purify: If the player shoots and then ults before the shot lands, the shot will not activate burning. Conversely, the final shots from the ult may inflict burning.
Purify: The Blastoff upgrade also activates burning.
Disorient: Does not stun in correct area when blast hits a player or player owned object such as a shield.
Disorient: Not garunteed to stun in correct area if rapidly moving crosshair while firing.

Ana
Life Link: Activates on healing dealt by ult.
Quantum Dart, Finish Him: If Ana scopes in, shoots, or uses Biotic Grenade before the sleep dart lands, the upgrade effects will not take place.
Quantum Dart, Finish Him: If a player is still being damaged by Ana's primary fire when she shoots her Sleep Dart, the upgrade effects may apply to that player.

McCree
Hot Streak: Bonus damage also applies to Flashbang, Quick Melee, and the first shot of Fan the Hammer.
Hot Streak: Bonus damage persists after death.

Sigma
Channeling: Continues if Sigma is stunned out of ability or cancels it.

Lucio
Rave: Lucio loses jump boost instantly if he is wall riding while activating Rave.

D.Va
Hydraulics: D.Va loses speed boost temporarily after using boosters if she cancels early or is stunned out of it while holding primary fire. Speed boost will be regained at the point the boosters would have naturally ended or if D.Va lets go of primary fire momentarily.

Widowmaker
Quick Escape: Can be activated if player speed is fast enough even if the hook does not attach to anything.
Poison Tip: Poison damage is applied on the next instance of scoped damage even if the player misses his next shot after using Venom Mine.