As noted above, attrition is the likely reason for the "holes in the program". It may also be related to people coming in and out of the lab and having funding for another if they are short a certain year.
Nonetheless, residency is difficult, and surgical residencies are known to be especially so. Some will leave because they SOAPed into a surgical position and never wanted to be a surgeon, others are unhappy, others transition/transfer into a surgical subspecialty, some/few may leave due to illness or family concerns. If more than 1 leaves every year from the same program, then you should worry.
Also the VAST majority of open positions are for fellowships, many of which may be new, not accredited, etc. Fellowships often have open positions. I mean, not many people are applying for "Global Health" or "Advanced Surgery" etc.