MySQL/InnoDB constantly performs merge and split operations, and you have very limited visibility of them. But they can bite you, and bite hard, especially if using a spindle storage VS SSD (which have different issues, by the way).

This is an important point to keep in mind. In InnoDB you cannot have fragmented records, but you can have a nightmare at the page-extent level.

The sad story is there is also very little we can do to optimize this on the server side using parameters or some other magic. But the good news is there is A LOT that can be done at design time.
This presentation will illustrate what really happen and how the use of a proper schema design may help you.