You should probably homebrew them a feat
The immediate problem I think you've encountered is that simply letting them choose three gives them more features from their race than is published, and is thus unfair to the other players. A reasonable approach to solve this is by giving them that feature (here adapation) through some different character option. The most general such option you can hand out is a feat (which is taken instead of an ability score improvement).
When you look at the simic hybrid race option their notable features are darkvision and the animal enhancements. Comparing with the variant human option, which gets proficiency in one skill and one feat (of their choice) we can very roughly say that the animal enhancement feature is equivalent to a feat in terms of 'power'.1 Roughly is the key word here, so now starts the process of making a balanced, reasonable feat.
Since you only need the feat to give one more adaption, you might want to make it a 'half-feat', though the adaption might be powerful enough on its own. Rough suggestion of wording: 2
- Increase one of your ability scores by 1, up to a maximum of 20.
- Choose one of the Animal Enhancements from the simic hybrid's options. You can't choose an option you already have.
Once you have honed the feat to where it is at least play-testable (and clear this status with your player) you can allow them to take it, and you should open it up to the other players as well, and be permissive to do similar things for them. Otherwise you risk showing favouritism, which can rightfully makes people upset.
1: Notable things this is skipping over; the flexibility of choosing from a list, the fact that the variant human only get a net +2 to ability scores outside of the feat (which might not include one), etc.
2: If you thing this is reasonable, it might be worth passing through a homebrew review on the site, making sure that question adheres to our homebrew review policy. If you so, please link to this question and be a good sport and give any due credit.