Answering my own question in case anyone else has this issue.
If you update the <versionNumber> in your app.XML file, it has an effect on CFBundleVersion.
In my case, my <versionNumber> was 0.0.554. This caused the CFBundleVersion to be automatically set to 0.0.99 and I didn't know how to manually change the CFBundleVersion.
By changing <versionNumber> to 0.1.554, this caused the CFBundleVersion to be automatically set to 0.1.99. This change finally allowed me to update my iOS app.