That can be fixed. The problem isn't with the ripping process, and track 1 isn't being overwritten. It is just at the metadata lookup phase that MC sets the wrong track number, and probably other details, on track 1. That is probably because of what is in the MC Album database that gets looked up, YADB.
That data comes from other users, so someone uploaded bad data at some time, and you are suffering the consequences. Make sure that when you insert a CD to rip and MC offers you a list of CDs that match, you pick one with the correct data. To see the list rather than have the first match selected, untick the setting "Options > CD, DVD & BD > CD Ripping > Auto Rip CD Database Lookup Options > If multiple matches are found, choose the first one".
The fix isn't to re-rip the track, but to just fix the metadata on track 1. To do that you need to identify which of the two copies of track 9 is actually track 1. You could do that by playing the tracks, or looking at the filename which will be different and may include the track number, or at worst case, looking at the time the two tracks were created. The file ripped earlier will be track 1.
Once you know which is track 1, edit the metadata to correct it, based on the CD in your hand, and all is fixed.
Once done, please submit your fixed Album details to YADB by right-clicking the Album thumbnail and selecting "Library Tools > Submit Track Info To Online Database".
Or better yet, at the start of the ripping process, when all the tracks are presented to you, use the "Edit Disc Information" button to fix any errors and then process the rip. At that stage you can clearly see the track numbers and the filename on the CD, such as "Track01.cda". If you have the setting "Options > General > Online Metadata > Allow automatic CD lookup / submission" ticked, which it sounds like you do, your corrections will be submitted to the online Album database, YADB. You should have everything ticked under that "Online Metadata" section if you want to improve the data.