Change your filtering order or expand User filtering
TL;DR - Change your filtering order or expand user filtering beyond the Inbox. You could also remove email marked not as spam from the spam list, gmail normally ask if you like to do this for future emails.
Yes this is very annoying problem and twice as annoying when using other oauth email applications like mail washer. The first major problem is that you need to fix is the filter ordering. You run your spam filter in advance of user filtering and that means for items I am 100% sure is spam or unsolicited email gets sent to the Spam folder and not the the Deleted Items folder as I have setup on my filtering. Now instead of being unbothered by these specific emails I have twice as much work. When I use mail washer I have a very clean spam folder and so I can quickly see what is in my spam folder that shouldn't be or would be a false positive or email that should have arrived at my inbox or custom folder normally. But now instead of my filter for specific spam being moved to Deleted Items, it gets sent to the spam folder so it shows up in mail washer so I have to manually remove it in mail washer even though I have a filter in yahoo mail to delete it. And secondly, now this is where you have quadrupled the amount of work on falsely detecting subscription email. I receive email from service@mx.thelotter.com for the last year and is not spam and I had a filter to send all emails from that domain to my custom Lotto folder but now you are filtering them as spam and sending their emails to the Spam folder even though they have the verified logo. So I usually ignore these email except for a few that are essential but I receive on average 2-3 a day and want them all in my Lotto folder and this was automatic with no intervention but now as they go to the spam folder they appear in mail washer which is an annoyance and then I have to go to my Spam folder in yahoo mail and mark Not Spam, it goes to my inbox and now I have to manually move it to my Lotto folder. It does not matter how many times I have marked as not spam, you are always putting them to spam folder for me now. So I get an alert in mail washer (annoying) when there is no spam, have to look and as it's a friendly email I have to then go to yahoo mail check my spam folder find the email, mark as not spam, go to inbox and move the email to Lotto folder... so congratulation on making filtering the most hands free experience possible .. well it would be if you put the user filter before your own spam filter or at least if you cant, can you at least run the user filters on the Spam folder as well as the Inbox after so 1) I don't see emails in mail washer that I have made a filter in Yahoo mail for sending items to the Deleted Items or Custom folders and 2) when you mistakenly identify an item as spam that I have a filter setup for it and have marked as not spam about 20 times now so I do not have to ignore in it mail washer and the have to go in an manually move it.
idk it seems obvious to adhere to user filtering before your own or at least run user filter beyond the Inbox when email arrives at folders .. I though it was bad enough when email I was deleting was getting sent to Spam but now email I want to keep are getting sent there. If it wasn't for this I would have next to no emails in my spam folder and can quickly see the occasional false positive.

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Charles McCarthy commented
Thank you! It seems my filters are working again or at least that domain is off the spam list. I'll have to check it later with some new filters for Deleted Items as I didn't continue with creating newer ones when they were being overridden. Regardless if you see this in future, consider making the changes as it would help keep the spam folder cleaner so instead of having to quickly parse through 20 items every other day in my Spam folder or 80 something at the end of the week if I neglected looking for a while. With this 99% of emails are deleted with mail washer so when I go to look or check things, there is usually just none, one or two emails in the spam folder and I can very easily see if there is a good or wanted friendly email. Anyways again, Thanks!