I had a similar experience with the aftermarket decals I used on the Airfix Hurricane I built that was part of the 100 Years of the RAF group build. It was coded LR * R.
The RAF roundel markings were slightly off registration and you could see a small white "ghost ring" where the blue colors met together against the camouflaged background. I had thought about trying to do a touch up paint, but then realized two things would likely happen. First the colors wouldn't likely match, and secondly my skill set is not good enough to do this and make it look round with sharp lines between the colors.
It is especially frustrating to get to this point and have something like this happen. In the end, my friend Paul Barber @yellow10
was kind enough to send me some replacement markings all the way from Australia ! He had the perfect match in his spares to save the day. Here's a link showing how I removed the decals using tape to pull them off should you be interested.
https://imodeler.com/groups/100-years-of-the-royal-air-force/forum/topic/a-pair-of-1-48-early-hurricanes-airfix-mk-1-and-a-classic-airframes-cloth-wing-version/?topic_page=5&num=15
Once the new decals were installed, I was very happy with how it looked.
I have been wanting a good reason to build up the two new tool Tamiya 1/48 scale Spitfires, and finish what I have started with the remaining ones in the stash. Thank you for the inspiration !
Your Spitfire is looking fantastic.