No explanation is given for this discrepancy. Given that Thanos is in possession of the Space and Mind stones (granting him what essentially amounts to near-omniscience) and given that he's a pretty honourable guy (in his own twisted way) it seems unlikely that he's lying to Gamora.
That being said, it seems more likely that the Nova Corp's records about Gamora's home planet are simply incorrect. If they're not in regular contact with her planet then they may be relying on secondary sources of information that she hasn't bothered to put right.
We may now know what director James Gunn was referring to in an interview he gave prior to the film's release. He and the VFX team apparently used information from the comics (in which Gamora's planet was destroyed by Adam Warlock) when they wrote the text for the mugshots, not realising that this would conflict with a later plot-point that he wanted to make.
“I’m writing Guardians of the Galaxy Vol. 3 and I finished the first draft of the treatment yesterday. I’m excited about it. I feel really great about it. But there’s one little thing that I had in the first movie. Now, Marvel Canon – MCU – is crazy. There’s the 616 universe which is the Marvel Comics Universe, which people get hung up on that canon, and then there’s the MCU, The Marvel Cinematic Universe, which has a separate canon (inspired by but not exactly the same as the 616.) I did something in the first movie of Guardians where it was in the background but it was distinctly there, and people know that it’s there. And I’m like goddammit. Because I have a really good storytelling reason for breaking the canon, and I stayed up last night figuring out if I’m gonna do it or not. I still don’t know.”
“I’ll actually tell ya. In the first movie there is the mugshot sequence where the characters go through and they’re going through the mugshots and having their picture taken. And the Nova Corps has information about each of the characters coming up on their machinery. Those things are something that your average viewer doesn’t see at all. But there’s a lot of background I put into those things about who they’ve worked with, where they are from, what’s going on. And it’s one of those things that I’m thinking about changing.”
James Gunn May Break His Own MCU Canon in ‘Guardians of the Galaxy 3’