The cause:
There is a cooldown between the time the game allows you to absorb notes while holding down absorb.
The issues it causes: (TLDR below)
The game never communicates that this is the case, and since there are so few times that the game clusters enough notes for this cooldown to matter when it does happen (such as Red Gnome battle) I constantly see players that are playing the game try to hold to absorb those lanes, only to take damage. These clustered notes are usually very brief, I don't really see the harm in letting them be absorbed since you'd only be absorbing a few extra with it allowed. And it's not even a consistently happening issue: its semi-random because the timing that you begin holding absorb will change if it damages you mid absorption or not, and I believe this has happened to me a few times in some regular battles (though I cannot remember which) because of said timing making it random and hence hard to catch. This issue is also what caused players to endlessly die at the end of the blackhole fight over and over if I recall correctly... they had to be re-arranged to fix it. But in game bugs are just the tip of the ice burg, because this has the potential to break all mods until it is fixed. Players creating custom battles probably won't even know this cooldown exists, and hence will cluster notes closer together than they are supposed to despite the clear intention of them being able to be held to be absorbed. And once again, the slight randomness will cause mod creators to not catch this, so it WILL plague all future mods unless every modder is told about a mechanic that the game never mentions.
The fix(?):
Just remove the cooldown entirely when holding down. I think the cooldown exists while not holding to prevent players from absorbing two lanes at once with skill, but only disabling it while holding/not moving would fix that easily. If it causes visual weirdness... a functional game is more important.