So you have some that come in as 00:00 and some that come as 00:00:00 ?
Inconsistent data is the root of all evil in Excel. It really is.
Here's the problem now.
Time has 3 components, hours minutes and seconds.
If excel is presented with a time value, but only given 2 of the 3 time components,
Then it assumes this to be HOURS and MINUTES.
Basically, someone decided that a person is more likely to exclude seconds from a timevalue, instead of hours.
So 2:30 is more likely to be 2 hours and 30 minutes instead of 2 minutes and 30 seconds.
That is why formatting as hh:mm has worked.
But now if some are coming in with all 3 time components provided, then this will no longer work.
You'll need some method to tell the difference between which format has been presented to Excel.
Or even better, work with the source data so that the times are reported the same way for all records. Either 00:00 or 00:00:00, not a mixture of both.