There was a listening exercise on Duolingo that had "Il a déjà terminé", but could it have been "il l'a déjà terminé" as well? As it was a "type what you hear" exercise, I put in "Il l'a déjà terminé" but was marked wrong for that. If there's a liaison between "il a" shouldn't these two sentences be pronounced the same?
They aren't pronounced the same, especially in an academic or formal context. There is a liaison in both but in the second sentence, the /l/ is at least slightly geminated although it might not be obvious in casual speech, especially as the /i/ or the /il/ might me dropped leading to /la.dʒa.tɛʁ.mi.ne/ where both sentences are undistinguishable.
Here is an example of such gemination (36 min 37 s)
No, but it's a good question. In the case of "Il l'a terminé", the le/la contraction between the "Il" and the "a" is pronounced together with the "l" sound of the Il. Basically, you hold the "l" for (something like) twice as long! Of course, when speaking quickly (much faster than Duolingo speed though), it will be difficult but doable to tell the difference.
In current French the difference may be audible or not depending on... where the speaker is from. Inhabitants from south of France usually pronounce clearly il then either a or la. Inhabitants from north of France will elide the second l and pronounce both as ila, specially if they are speaking quickly. The difference is close the the zones called langue d'oc or langue d'oil, for the way oui (yes) was pronounced in old French. And the difference still exists because before 1950 children in south of France learned French in school but spoke Occitan at home. My grand mother died in 1977, and could never speak French, only Occitan.
Said differently in Marseille or Toulouse, the pronounciation will be clearly different, but in Paris or Rennes, it will be the same.
That being said, in correct French, the pronounciation is expected to be slightly different.