So as the tournaments I hold were going on I was discussing with a few of the regulars about something that I’ve noticed recently. When I’m being put in a combo and a person counterbreaks when I press HP+HK with full instinct bar, It prioritizes the Combo Breaker over popping Instinct. Not sure how it would pan out but my immediate thought is to put the counter breaker on whiff, pop instinct, then DP to get distance back all while still keeping potential damage as is. So I’m more interested into what the community thinks about this point as myself and some of the regulars agree on this a bit.
It’s entirely possible you’re trying to activate instinct while you’re still in hit stun frames from your opponent’s last attack as he counter-breaks, which would explain why you get the lockout. If that’s the case, it shouldn’t last long though since your opponent dropped his combo with the counter-breaker, hopefully giving you the opportunity to counter-attack.
Yes, be careful with this, as this actually catches most people. Usually if you see someone Whiff Counter Break, then a FULL second goes by and someone gets locked out, it’s usually that they were still in hit stun. Be careful! 
What you are suggesting is that you should get safe combo breakers on heavies if you have instinct meter. If they didn’t counter you would get a breaker and if they did you would get an instinct activation and free punish (which would make just doing a DP a huge waste btw).
The fact is that you pressed the buttons for a combo breaker when they did a counter breaker, your intention may have been to do something else but the game can’t know that.
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Yep, he’s right. If you want to pop instinct, do it when you’re absolutely certain, without a shadow of a doubt, that you’re not getting hit by a combo. 