The first is that these bubbles appear repeatedly in my negative
As
@Nicholas Lindan mentions, they are due to excessive foaming in the developer, but this problem also suggests a lack of agitation and/or insufficient developer volume. Generally with a rotary development process, foaming doesn't matter since the foam is continuously displaced by liquid developer, so it doesn't matter it's there. Color developers often have wetting agents added to them which tend to foam, so it's natural for some foam to be present in the developer.
This brings the question:
1: Which tanks are you using and how much developer volume (milliliters) are you using? If you're using insufficient developer for your tank, you can run into problems like these.
2: How long does it take between the tank being filled with developer and rotation starting? If it takes too long between filling the tank and commencing rotation, you can risk uneven development. It should only take a few seconds between filling the tank and starting rotation.
3: How much time is there between dumping the developer and pouring in the next bath (stop or bleach)? If this is too long, foam can remain on the film and the edges of the bubbles will cause additional development in these areas.
The second problem is that my negatives are coming out very clear
This points to either of the following, or a combination:
* Developer not on the temperature you think it is (too cold)
* Insufficient developer volume (see above)
* Insufficient developer activity due to it being too dilute or underreplenished (e.g. developer reused for too many rolls of film)
* Too short development time; C41 development time at 38C/100F is 3m15s nominally.
Judging by how thin your negatives look, this is not an issue of temperature drifting by one or two degrees; you wouldn't get this much underdevelopment it that were the case. It's either a massive deviation in temperature (5-10 degrees) or some other factor at play. I put my money on the latter.
It will help if you could answer the questions above and indicate to what extent you've already tried mitigating the causes that were mentioned thus far for underdevelopment.
And welcome to Photrio!