Good afternoon, Erin!
Common causes for this to occur include the following:
Spam filters triggering off of:
-> Email Content (javascript, key words, formatting, etc.)
-> Amount of emails being sent to or sent from a particular address (typically trips free email services like gmail and yahoo)
-> Users flagging the email as spam or malicious
-> Overly strict Spam filters (locked down corporate networks)
Typically you don't see the tracking code causing spam issues but that's not to say it couldn't happen.
Is there something you're seeing in particular that's raising a concern?