I'd have to see it in person (or good clear detailed photos) to assess what to do.
It could be that the decals were applied over a clearcoat and then cleared over. Removing the decal leaves a hole in the final clear coat. As mentioned above, rubbing compound is a good way to diminish this "hole". Maybe try 1500 or 2000 grit sandpaper, then rubbing compound, then Finesse, then glaze.
But if the decals were applied to the bare titanium, then clearcoated, you will have "holes" that can't really be fixed easily. You may want to consider having a clearcoat sprayed over the whole frame to eliminate those.
Or...you could have the frame stripped, powdercoat clear (which sticks much better to titanium than paint) apply new decals, spray clear paint over all that. All beautiful again and no "holes"!
This reminds me of the anodized BikeE recumbents I used to rent/sell. When they came to the shop, I applied cut vinyl lettering with shop name/phone #/website. A friend bought one when I closed the shop. 5 years later I ran into him still riding the bike. He had removed the lettering. But it had been on long enough that the anodizing had faded a few degrees. So when he removed the lettering, the "ghost image" was still there, in fresh bright anodizing! And like a "Candy" color, there is no way to "fix" it!
Good luck with that! Let us know what works out for you.