A simple practical reason is that the volume of known files that has MD5 or SHA1 hashes is huge compared to SHA256. It's preferable to have something collision-resistant, but also if your goal is to simply be able to identify files, and MD5 or SHA1 checksum can be fine. That will change over time, but realistically tons of AV scanners and tools like this need to support MD5 or SHA1.
Of course, if you're generating new files that you know about or checking existing known good files, one would include the SHA256 and SHA512 with it.