MC puts the Season and Episode numbers into the file name if it finds that information in the EPG data.
Bad quality EPG data is always going to be an issue. But it could be that SD are just going through a bad patch. I thought SD either provided good data, or none at all for those tags, when using their standard API. If you have the paid for version of mc2xml and are using that for SD, set it to use the JSON interface, rather than the standard API. I believe that the JSON interface provides better data, including Season and Episode numbers.
Search the forum for how to do it. CountryBumkin has written it up.
Note: While you could use the tagging by Recording Rule function to remove the bad data, that happens after the file is named I believe, so that won't help. Trying to change the file name by tagging rules is also possible, but I'm not sure how much success you will have, and what other problems that will create. Certainly you would have to run the "Get Movie & TV Info" function again after the shows are imported. Also, there are third party programs that will "clean" EPG data. You could try searching the internet for them, and trying them out. Most are old though. Again, it would complicate your EPG collection system to need to run multiple programs to collect and then clean the data. Better to fix the problem at the source.