Cycling isn't the issue. Runners when they actually start REALLY training have this issue. They need to learn to slow down. Too many think they're running "easy" pace when in reality, while it feels easy, they're well into tempo pace and running way way too fast on their easy days.
Slow your roll, its not cycling, its you.
Beginner cyclists do this, too. It's all go, go, go. Even when it feels easy, it's probably at threshold and encroaching upon overtraining.
A recognize that this post is a little old now, but I have had some additional experiencing I would like to share regarding getting comfortable in the water.
The tl;dr version is: Get out of your own way.
If the OP is anything like me (and the fact that he's attempting to analyze and diagnose potential issues would indicate that he is)--and for anyone else in the same arena--there is a lot to be said about overthinking leading to relaxation and breathing issues.
Most of this insight came while taking Fundamentals, but the two key points I'd like to share is that:
1.) I cannot stress the importance of having a skilled diver present to physically manipulate your body into proper trim so you can feel what that is in the moment.
I can't see myself to know what I look like in the water, and watching a video later doesn't help my muscles now what horizontal trim feels like. Being physically put into neutral trim helped me realize that I was over-tensing every muscle in my body (and, thereby, using far more gas). I was arching my back into a hyperextended skydiving pose and fighting against myself to maintain position in the water column because of it.
2.) Sometimes not focusing on breathing is key.
During Fundies, my buoyancy control and gas consumption improved significantly when I was task-loaded. Tending the SMB or being deco captain or (not during Fundies) being absorbed by my camera, I was able to maintain buoyancy and breathe easier because I wasn't fretting about those things. I was just doing then.
Looking back, I should have realized this was the case since my first two Discover Scuba dives. Dive one, no task loading. I was all over the map from 40 feet to 20 feet back to 40 then to 30 then 10, and I sucked my tank down to 500 psi while my wife and instructor still had 2,000 psi left. Dive two I took my camera and focused on photographing things. No yo-yoing and I had only slightly less gas than the other two by the end of the dive.
My tidal volume still needs work. I still tend to over-inflate because that's how I breathe on land, but my average RMV has dropped from 0.75 to 0.55 in the two years since I've been certified. That's 84 dives, or roughly 78 hours.
Practice and good training have helped a lot, but so has observation and being aware of myself and my behavior in and out of the water. (It isn't a new tendency for me to have a better skill at something when I'm task loaded, for example, and I should have thought to leverage that sooner.)