There seems to be an issue with the way the filter loaders work, as an example when using the Ultra Express Filter Miniloader, I can set some filter requirements for it, however when none are set it still pulls from the source. There's also the issue where when I copy & paste, it will show the filter settings, but they don't apply (clicking on the filter miniloader to re-set the filter settings will then clear it), as well as I've run into a bug where the filter miniloader will stop filtering and I can't open the filter settings, it will then work as a regular miniloader of that grade.

You can fix the upper problem by just copy-pasting the actual miniloader with the filter already set to the one that doesn't work, however this does make large blueprints quite annoying.

Does this happen reliably when placing a blueprint? Are there any specific steps that cause this to happen?

not sure how repeatable it is as I mass upgrade all my belts once I have the next tier automated, however I know there's sometimes the issue with the bots fast-replacing them.

I've found something that might help, which is that when blueprints are placed with the miniloaders, there is no last user, and thus the filter is not set, however once I set the filter and it shows the last user as my name, the filter will remember its setting.
Not sure if that helps.