How do I fix a missing transaction from my credit card?

Are you sure it didn't download and automatically merge with your manual transaction?

In any case, all that matters is that your Quicken register is correct. If you've checked your register against your credit card, if your Quicken balance matches the credit card, it sounds like you're in good shape. (I know you probably are looking for an explanation. If it didn't download and auto-match, I wouldn't worry about it unless this becomes a recurring problem.)