While I don't want to rule out the possibility of it being a bug, I will say that it is an intended feature of his kit.
Here's the reason why: Master Yi's alpha strike can be used as not only a dodge tool but also a disjoint tool.
Disjoint vs Dodge
**Dodge ** is pretty self explanatory, you see a skillshot/ability coming you press q well BEFORE it hits to become untargetable and dodge it (both damage and duration of ability).
Disjoint is when you press q as soon as the skillshot/ability connects with Yi to limit the duration of its intended effect. However, in this scenario the ability is still in effect on Yi once he comes out of alpha... but the duration of the abilities effect has been reduced by the amount of time he has spent in that alpha.
Examples include: Lux snare, Morgana snare, Warwick (old) ult, Ahri charm.
The disjoint functionality IS an intended feature of alpha strike and is difficult to pull off requires precise timing (old warwick ult only gave 1 frame before activation). Think of it like a second way to dodge cc, BUT NOTE: Disjoint only nullifies the DURATION but not the DAMAGE. To nullify both damage and duration you need to Dodge.
Here's a video from the Yi-sus himself better explaining disjoint:
https://youtu.be/heneW2EdGzs
EDIT: MAKE SURE TO WATCH THE VIDEO AS IT EXPLAINS IT ALOT BETTER THAN I