Here's an excerpt from a recent score log of mine:
Average Core Remaining (%) 87
Depth 10 Exit 58
Depth 9 Exit 100
Depth 8 Exit 97
Depth 7 Exit 92
Depth 6 Exit 86
Depth 5 Exit 93
Depth 3 Exit 168
Depth 2 Exit 91
You'll notice there's no Depth 4 exit, and it says I had 168% core on Depth 3. I went into upper caves on -4 and got to -3 that way. I suspect that's the cause of the problem.
e: Yep, it's definitely caused by going into branches:
Average Core Remaining (%) 71
Depth 10 Exit 68
Depth 9 Exit 24
Depth 8 Exit 96
Depth 6 Exit 164
Depth 4 Exit 75