There is a gap in this series where nine issues were published by Holyoke. See http://www.comics.org/series/269/
This series has a somewhat complicated and confusing numbering scheme, but most of it becomes clear when considered alongside Cat-Man Comics, which was published by the same companies throughout the run of both titles.
See the tracking notes for a discussion of the theories behind the starting indicia number of v1#7. Things continue just fine through v1#12, after which they reset to v2#1. This is a common enough occurrence, and only looks at all strange in conjunction with other renumberings. See the Cat-Man entry for a discussion of how this lines up with other Holyoke events.
The jump from v2#4 to v3#9 seems random, but Frank Motler observes that v3#9 would have been the correct number for the Cat-Man issue that came out that same month. That Cat-Man issue was numbered v2#6, and if one assigns v2#5 to the month in which Cat-Man produced its first issue under Et-Es-Go Magazines, Inc. but Captain Aero did not produce an issue, then it appears that Captain Aero and Cat-Man simply switched numberings.
Captain Aero stops using cover numbers with v3#13, also the last Et-Es-Go issue. This number was also "borrowed" by Cat-Man the prior month for its first non-cover-numbered issue, although this time it returned to its regular sequence the following issue. Captain Aero then resets to v4#2. The fate of v4#1 is something of a mystery. It could have simply been forgotten, or somehow considered to be synonymous with v3#13 on the grounds that the volume should have reset after issue #12 as it did between v1 and v2. All of this is pure speculation, however.
Captain Aero put out one more v4 issue with no cover number, and then abruptly jumped to whole #21 (same in the indicia and on the cover). This jump could have been carelessness, or the mismatch here and with a one-issue-backwards jump to whole numbers with the next issue of Cat-Man may both be explained by something else.