Contacts are disappearing from my list and I did not delete them.

The three documented causes

All three run without a person clicking Delete on that specific contact.

1. A hard bounce. systeme.io states that addresses identified as fake or non-existent are removed from the contact list automatically, once they are identified as such.
2. Automatic list cleaning. A weekly setting under Settings, then Emails, can be configured to delete, rather than unsubscribe, anybody who has not opened an email in 1 to 26 weeks. Once switched on, it runs every week with nobody touching it again.
3. An expired double opt-in. Where a form has double opt-in switched on, a contact who does not click the confirmation link within 24 hours of registering is deleted automatically, not merely marked unconfirmed.

Working out which one it was

Start with the Recently deleted bin, under Contacts in the CRM menu. Every row there carries a removal method alongside the deletion date and the email address, kept for 30 days, with a Restore button beside it.

What systeme.io's documentation does not say is whether all three mechanisms actually file into this same bin, or whether a hard-bounce removal or an expired opt-in bypasses it. No article connects the bin to any of the three causes directly. Checking it is still the fastest single test, because if the contact is sitting there, the removal method column answers the question outright.

If the bin is empty for that contact

Two things are worth ruling out before assuming a new, undocumented cause. First, whether somebody else with access to the account, an assistant or an admin, removed the contact by hand. Second, whether the address ever confirmed a double opt-in form in the first place, since a contact deleted for missing that 24-hour window looks, from the outside, exactly like a contact who never signed up at all.