The file naming is indifferent to MVC or any design patterns.
Including ".inc" and ".class" was an old practice that even many old PHP programmers disagreed with.
Basically, these letters only helped to identify what kind of file it was. If it had ".inc" in the nomenclature, it meant that it was an include file, ie it should not run directly. Idem for ".class" types.
There are also ".func" and ".cons" types, for functions and constants, respectively, and there probably must be others, but these are the best known.
Normally these files should be kept in a private access folder, not accessible by the user. But not everyone could follow this recommendation because N reasons. Lack of knowledge or resources (the host would not allow it).
In general, you'll find nomenclatures like
file.inc.php
file.class.php
file.func.php
file.cons.php
Some omit%% of the end, but that may be a bad idea because you can expose the codes in public if the environment is not well configured.
Old and heavily used systems, such as PHPMyAdmin, still use this practice.
It is worth noting that this is not also bad practice. It is merely a matter of opinion / choice of who creates the project. The important thing is the project to be well written, well documented and organized. The nomenclature matters little as long as you know what you are doing.