This is, I am afraid due to sampling effects related to the number of populations, there are two alternatives here:
1. You think that you have 2 populations overall (i.e. you sampled 2 out of 2 in the wild), and in this case the CI that Lositan is computing is not trustable
2. You think that you have more populations overall. In this case the sampling issue disappears.
So, Lositan is not appropriate if you have 2 populations in the wild, so I would recommend not to use it. But, if you are sampling 2 populations out of many, then you can probably still use it. Of course, how many populations you have might be complex to estimate, but if you are sure you have more than ~10 wild pops, the results should not vary much.