I was surprised to see a few 15 minute episodes that were combined together for one half hour in episodes 4 and 5. Looking at the episode guide there is one more of those, then they are dropped. On the other extreme, season 2 has a 5 part episode.

I know that the 15 minute episodes (https://www.hpb.com/products/punky-brewster-683904451453) were done because NBC at the time had the broadcasting rights to the American Football Conference in the National Football League. NFL games commonly overrun past 7 o'clock on the East Coast. This would naturally cut into Punky Brewster's Sunday evening time slot. So instead of preempting Punky Brewster outright or joining the show in progress (https://www.mentalfloss.com/article/68748/12-very-special-facts-about-punky-brewster), NBC produced (https://tvtropes.org/pmwiki/pmwiki.php/Trivia/PunkyBrewster) 15 minute episodes, so not to disappoint the show's young (https://www.everything80spodcast.com/was-punky-brewster-too-intense-for-a-kids-show/) demographic, who weren't interested in football.