Your idea that the blocks of time should be 'non-overlapping' is basically right. It's not clear what kind of data you're talking about. But for example, say you were examining variation in rainfall over time. You measured the rainfall at hourly intervals. If you really thought one second's worth of extra rainfall would introduce an intolerable error into your research -- and that this error wouldn't be swamped in any case by other much larger sources of measurement error -- then you would be sure to define one hour as 3600 seconds and not with reference to coordinated universal time (UTC), which inserts leap seconds.
Alternatively, if you were somehow tied to defining time with reference to UTC, then you could make a correction to the hour containing the leap second, probably multiplying your measurement by (3600 / 3601) (which would only reduce your measurement by 0.03%).
But yes, you are probably over-thinking this! Leap seconds only occur less than once a year on average, and will be ignored by timekeeping devices that aren't linked up to a UTC source.