Recently updated the company to all IMAP accounts, but now every account is synced? There are two computers at my company that are Macs.  We just both upgraded to El Capitan OS, and had to change our mail accounts from POP to IMAP to work with the Parallels that we run.  Ever since we did that, both of our mail accounts have been in sync with one another.  Whenever he reads an email on his computer from our General Mailbox, it shows up on my computer as "Read" already.

It's getting very frustrating, because we feel as though things are starting to slip through the cracks.

Is there a way to reverse this?
That's what IMAP does, it keeps the client state in sync. So it's doing exactly what it should. You can switch back to POP to get the old behaviour.