I noticed this too bug reported it. I find the Y lmb kinda awkward. Wish it just had a pet bar.

Since the beginning of the game I changed my keybindinds. My mouse hand is strictly movement and my left hand is strictly combat/interaction.
Thus I remapped the A button to attack.
My pets will attack with Y followed by A. This has worked flawlessly in a couple of three mob fights I have soloed and once in a five mob fight I soloed.
This simple change has made my favorite play stlye even more effective. I'm a sorc tank, built on the premise of regenerating magicka. In solo gear, I run five cloth for the crit/regen/resist that it offers. My stamina is reserved for blocking and interrupting and the occasional cc break if I miss a block.
I literally have Clannfear, Matriarch, Bound Aegis and Inner Light on my hot bar and put one and only one attack power on button one. That's usually volcanic rune but can sometimes be thundering presence or even velocious curse.
This allows me to concentrate my quickness to react to things that I can block, dodge or interrupt. Block and interrupt are part of my offense. Both cause off-balance and that gives me a chance to reset my button rotation, take stock in the situation and maybe have pets switch or even just get in a few free whacks.
My total time per pull has been cut in third. With my new focus on block and interrupt I can crush a caster. With the new Y button I can be sure to put the pets on the two-handed mob and that they will likely stay on him.
Before the Y button, I could put the pets on the two-hander, but they tended to come over and stick their nose in my business with the caster. This agro switch had some very nasty side effects. Once the pets lost interest in the two-hander, the two-hander would decide to hit me with a stun/knockback. Suddenly I would be defenseless with both the two-hander and the caster pouring their might down on me.
I had to drop this play style because the number of deaths this agro switch was causing.
With the Y button, I control the agro switch. I interrupt the caster and while he is off balance, Y him and personally switch to the two-hander. I usually do this in the last third of the casters health bar. The pets finish the caster fast enough and I am focused on blocking the two-hander.
Admittedly, I havent bugged on the Y button yet but this may be because I remapped LMB to a keyboard key.

It is unfortunate that as fast as the fix something, they also break something else. This game has been plagued from day one with issues, and quite frankly is not getting any better. While levels 1 - 50 are pretty good in terms of PVE solo play, the MMO model seems to be almost an after thought. With some many great games to draw ideas from, why in some cases did they re-invent the wheel and in some cases, made the wheels square instead of round. Over all since launch I give this game a 6/10.

This issue was reported on the PTS forum:

http://forums.elderscrollsonline.com/discussion/107861/pet-command-issue-winged-twilight#latest

Read the last post:

"There's a larger issue with the new pet controls that I haven't seen mentioned yet. It seems that once you start using the Y+l-click to attack and Y+r-click to disengage, you must then use those controls all the time thereafter. Unless I'm just missing something (and I did not see any 3rd option called out in the patch notes) I see no way to return to the default pet control setting afterward."

My pet does nothing now. I have to re-log to get it to attack.