The phrase often carries a tone of resignation or acceptance that things went wrong without blaming anyone. He missed his flight, but these things happen.
Pro Tip 2/3
Gentle Consolation
Use 'these things happen' to console someone gently when something mildly unfortunate has occurred. You forgot the tickets at home? Well, these things happen, let's try to enjoy what we can do instead.
Pro Tip 3/3
Unexpected Events
This phrase is suitable when referring to events that are unforeseen and not typically the result of someone's actions. The sudden rainstorm ruined our picnic, but these things happen.