I have several flagged emails in my inbox that don't show up in my flagged mailbox. How can I fix it so that all of my flagged emails are in the flagged mailbox?

You could try unflagging, then re-flagging them.

It could be that Spotlight failed to index them. In that case you can try rebuilding the Mailbox.

Another option is to just create your own Smart Mailbox to show the Flagged messages--I don't know if it will resolve the problem, but it might. If the Spotlight index is not complete, then this will fail just like the built-in mailbox.