For a particular Transition and a particular Replicate, I would expect that "Interpolated Times" and "Interpolated Intensities" would have the same number of values in them.
Furthermore, all of the transitions for a particular Precursor in a particular Replicate should have the same Interpolated Times as each other, because the purpose of the interpolation is to prepare for peak detection by putting all of the transitions on the same time scale.

In your attached CSV file, which Transition and Replicate are you looking at where you see 2389 times an d1246 intensities?

If you are writing software to analyze this report, you will probably find things easier if you uncheck the "Pivot Replicate Name" checkbox in the Customize Report dialog. Doing that will ensure that each Replicate appears on a different row.
If you are seeing different numbers of intensities and times the most likely cause is that you're not looking at the same Replicate.

-- Nick

From what I can tell, none of the transition, sample pairs have the same number of times and intensities. For example, here is a code snippet where I explore this:

Here is an Excel spreadsheet where I added columns to count the number of commas for the "Times" and "Intensities" for the first replicate for all of the transitions.
The numbers are always the same.

In your code snippet, I think that "len(rts_test)" is actually the length of the string "rts_test".
If you want the count of values in that string you would have to count the number of commas.
Claude suggested doing the following to convert "rts_test" into a list of numbers:
np.fromstring(rts_test, sep=',')
-- Nick

Ah that did it! I was expecting ints but the document recorded intensities and RTs as strings. Sorry for the dumb question!