ein/eine/einen/einer/eines/einem all mean "a/an/one"
Einen doesn't exclusively mean "an".
The difference is simply gender and case.
"fliegen" (not capitalized) = the verb "to fly"
Eine fliegen ist ein Insekt = doesn't make sense..."A (to fly/flying?) is an insect"
"Fliegen" (capitalized) = the plural noun "flies"
Eine Fliegen ist ein Insekt = doesn't make sense... "A flies is an insect"
The given English sentence is about a single fly. You must translate it to singular. If you wanted to use the plural, it would be "Fliegen sind Insekten".
Hope that helps.