Hi theemurman,
I agree with Barry about the Mysteries of 'Date & Time' and 'Duration' formats in Numbers. They can be confusing.
Here is a way to get over the "crossing midnight" problem when Start and End times are both entered on the same day.
Test for a negative Duration and add one day (+"1d")

Columns A and B are formatted as Date & Time (Date None).
Enter the Start and End times and don't worry about the date. Just do it.
Column C is formatted as Duration (Custom Units > Hr Min).
Formula in C2 (and Fill Down)
=B2−A2
Now test for the "crossing midnight" problem.
Formula in D2 (and Fill Down
=LEFT(C2,1)
If there is a negative Duration, the leftmost character wil be a minus "-" sign.
Formula in E2 (and Fill Down)
=IF(D2="-",C2+"1d",C2)
This tests for a minus sign.
If the Duration is negative, the formula adds one day (+"1d") to give the correct result.
If the Duration is positive, that is the correct result.
This will only work for two consecutive dates (only one "crossing midnight")
If you follow Barry's advice and enter the Start and End times on the actual Start and End days, this is illustrated in Row 8.
Start time was entered on 29 June. End time was entered after midnight (on 30 June). The formula will work because the dates are different (no negative Duration).
Regards,
Ian.
P.S.Midnight may show as 00:00 or 12:00 am depending on your cell format (and perhaps Region settings).