First you need to remember that parts are user submitted and may be wrong. I and others tend to look over parts newly posted and check them for accuracy and obvious flaws but that isn’t always done
even in parts in core. I’m working on a python script that automates this and eventually hope to clean up core but that’s likely a ways off.
I have made changes of some kind to about 6 of them and I don’t remember which one had small holes. A search for lolin in the forum search bar (always a good place to start) turns up this one which mentions small holes but there may have been more than one.
a search for esp32 turns up even more posts. If you have the name of the part you used I can probably tell you if it is one of those that I changed. There are many different versions of these boards some in odd sizes (at least one is 1.1 in wide rather than the “standard” .9in)
No the gerber file has done that for you: In what ever this is (probably all the top view parts I made yesterday. in which case I probably should look at the hole sizes on them, given this 
) the lines after INCH are drill sizes
T102C0.038000 is the only correct one in the list, being the correct size for a .1 header pin which is what you want. .035 (IC leads) and .040 (1N4001 diode holes) are other common sizes. The weird ones in the table will usually get rounded up to the next higher standard drill size by the board house but are inf fact sloppy and incorrect. The leading Txxx value indexes the following table of x/y coords where that hole will be drilled, but usually you only care that the initial size table is correct.
; NON-PLATED HOLES START AT T1
; THROUGH (PLATED) HOLES START AT T100
M48
INCH
T100C0.037000
T101C0.032833
T102C0.038000
T103C0.037222
T104C0.039370
T105C0.020000
%
T100
X017489Y019218
X016489Y019218
… (many more)
Peter