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Posting the breakdown and details usually will help us help you sort it out. I can tell you that the loan is in a great position and helping, and that you should let one card report a small balance so that you aren’t penalized for having no credit in use and under active management - that alone can be worth 10-15 points.
For the loans it’s best to call in @calyx and @Anonymous - they are our go-to loan gurus.
Welcome @Anonymous !
May I ask who your servicer is? Your best bet at this point is to contact them and explain the situation and ask them to remove the lates since you were unaware that you were coming out of deferral. Some servicers are easier to work with than others, which is why I ask who the servicer is. Student loan reporting is covered by an additional law (HEA) beyond the FCRA, so some servicers will refuse to change their reporting without a lot of very strong nudging (or at all).
The reason you have so many loans is that generally each semester's student loan(s) is/are separate, so you'd have one for Fall Year1, Spring Year1, Fall Year2, etc. They'll split up further if they're different kinds of loans (particularly subsidized and unsubsidized).
For the future: If it would help you keep everything together, you could consolidate the loans into one (for free, through the Dept of Ed - not through any financial institutions), but you'd want to make sure you aren't going to mess up any payment history that's going towards potential forgiveness programs (though it looks like you're early into your payment). You would also have a new tradeline, but I don't know how much age you have at this point. The interest would be a weighted average, so you wouldn't gain/lose much of anything there.