I think this sentence is not perfectly grammatical. You can analyze it as follows:
龙舟队 The Dragon Boat Team
分 (divide into, assign to)
哪个 which (one)
两个组 two groups
It doesn't sound grammatical to me mainly because 哪个 means "哪（一）个 which one", but the subsequent noun phrase is about "两个组 two groups".
We can probably read it as "which two groups", but then the Chinese would be “哪两个组”.
As additional evidence, Googling the quoted “哪个两个组” phrase yields a good 5 results, against 84k for “哪两个组”.
Anyway, putting it all together it becomes something like:
Which two groups is the Dragon Boat Team assigned to?
Which two groups is the Dragon Boat Team divided into?
In both these cases, I think 分组 is not a separable verb. Why?
In a separable verb the separable part is the object of the sentence (that's why they are also called verb-object phrases) but this object has a non-specific meaning (some linguists call it virtual or ostensive object), and as such, in English it's often rendered as a 1-valency verb. Compare:
我吃饭 = I eat
我跑步 = I run
Instead your sentence already has an object — or if you prefer, the subject of a passive form —, which is 龙舟队 ...unless you want to argue that 龙舟队 is who performs the division in groups. (The fact that 龙舟队 is the topic of a topic-comment construction doesn't affect its grammatical role.)
As a counter-test, can you rewrite 组 in a 把 + Obj. + V structure? You can't. Instead 龙舟队 can be placed after 把:
他把龙舟队分哪两个组 (ok) vs
龙舟队把组分哪两个 (???) (not ok)
So what is 组 then? I think it's the object of a 3-valency result complement structure. This is relatively easier to see if we rewrite the verb+result in a copy structure, instead of topic-comment. (This is similar to what you can do with degree complements):
(主语) 分 龙舟队 分（成/到） 哪两个组
This is my analysis. Any feedback is welcome.