You specified 1st level....a part of the game where its almost impossible to have a character be able to fly at-will, and even short term "flight" is rare. Any "mobility" enhancements are usually short term and are limited in use and i've never once seen an all-flying 1st level party in my entire gaming career, so why would I suppose the entire party would be flying in a 1st level proposed encounter?
Two goblins vs. 4 lvl 1 characters is an Easy encounter. You could maybe bump it up to Moderate if you considered the caltrops and barricades to be a big advantage for the goblins...but that's not enough to make this a serious test of the character abilities.
The PCs could have used Charm Person, Command, Disguise Self, Fog Cloud, Jump, Sanctuary, Silent Image, and the everpresent Hiding in Shadows to get 1 or more characters up to melee with the goblins with little difficulty. Those are all 1st level spells, fairly common, and with a reasonable expectation of success. It isn't like flight is so much better than any of those choices in this encounter (in fact hiding and sneaking is the best choice because its "free").
The point is...if the encounter drained some resources...then it did its job. It doesn't matter if it used some Ki points from a monk, some spells from the wizard, or some HP from the fighter. Its just some amount of attrition for the adventuring day.