Hey Chesse, welcome to the community:
It is hard to help with this limited ammount of information. Could you please make a reproducible example?
I am not completely sure, but I don't think na.omit works in the context you are using. To me, it is like more an argument to deal with NAs inside models like in nlme. not inside a data.frame or in the context of data cleaning/processing.
you should do something like:
mydata <- mydata[is.finite(mydata$hmsacld), ]
Unles na.omit is defined in a specific package that you are using and in its context. Note that I have used is.finite rather than !is.na because it will remove both NAs, NaNs and -Inf, Inf, a source of problem when fitting models, specially for novices.
Anyway, your original error points to factor problem, not to NAs. If you use quantile with NAs, it will vomit something like missing values and NaN's not allowed if 'na.rm' is FALSE. This is most likely due to you have some characters mistype. like an o where it should be a 0.... you can check it with is.finite, but please, provide a reproducible example so we can help you more.
cheers
Fer