I've noticed that other words that end with -bær ('berry') are missing a plural -er ending: jordbær, bringebær, blåbær, etc. It could be because 'et bær' is a single syllable, neuter noun and doesn't have a plural ending; that could carry over into the words ending with it. Either that or they could be irregular nouns.
If I'm having a hard time hearing it, I can usually catch the difference if I listen to the slow version. Eplet sounds more like epla. Epler may have a soft R, but it is definitely there. It also may sound slightly longer than eplet, because you kind of hear the R release, almost but not quite like eplera.