I came to US in 04/16/2016. Between 01/01/2016-04/15/2016 I didn't have Health insurance. I have chosen months which I was insured. It wasn't possible to have insurance from the begnining of the year.

If you spent 330 days outside of the U.S. within a 12 month period that includes all or part of 2016, then you can use that as your exemption.  There are other situations that are covered within this same realm.  Please see the attached screenshot.

I have spent in the U.S. 259 days. I came to US in 04/16/2016 on L1-Visa and due to that fact I couldn't have insurance earlier.

As mentioned, it's 330 days during a consecutive 12 month period that includes at least part of 2016.  Therefore, you arrived in the US on 4/16/2016.  So from 4/16/2015 - 4/15/2016, did you live outside the U.S. for at least 330 days during that 12 month period?

Yes, in that period I have lived outside the U.S for 365 days.

Yes, in that period I have lived outside the U.S for 365 days.

Then please use the exemption in bold above.  "Spent 330 days or more outside U.S."

So, you will say "yes" to a situation that waives it, then when asked which exemption you are claiming, that will be your option.