As this ELU answer indicates, the correct version of this phrasal verb is actually to home in (to head directly towards a target). But OP shouldn't let that bother him; quite possibly most native speakers use the "wrong" version.
So the combination isn't really in + on - it's home in + on. It occurs with other phrasal verbs of the general type [verb] in, such as...
I'll look in on you this afternoon (to look in = visit briefly)
We'll check in in the afternoon (to check in = confirm arrival - at a hotel, for instance)
The burglar broke in in the night (to break in = enter illegally by breaking a lock or window, etc.)
As those last two examples show, although it might look a little odd to some, there's nothing "incorrect" about repeating even the same preposition. The first occurence is part of the phrasal verb, the second is just a normal preposition indicating the relationship between verb and object.
EDIT: Per comments below, I've just changed "sound a little odd" to "look a little odd" in the above text. The stress patterns of normal speech mean you'd barely notice the same preposition occurring twice (one would normally stressed, the other not, so they'd sound very different). But in the written form it's distracting/off-putting for the reader. Suppose, as per @J.R.'s example, your first thought was to write...
I didn't understand what she was getting at at first.
In that particular case, you could just insert a comma between the two at's to help the reader along, but it's only a partial solution which won't always work. Unless you're committed to accurately reporting actual speech, a little rewording is probably better...
At first I didn't understand what she was getting at.