This first sentence has an error in it; you can’t use "en" in a simple context, that is where the referent has just been mentioned or can be elicited.

• Ils aiment les fruits ; ils en ont mangé les pommes.

• Il y avait toujours des fruits à la cantine ; ils en ont mangé les pommes.

  In a rarer context this becomes possible but is extreme.

• Il y avait une panière de fruits dans la cave; ils en ont mangé les pommes ; tous les autres fruits étaient verreux.

This will be said almost always differently, without "en".

• Il y avait une panière de fruits dans la cave; ils ont mangé les pommes (qui s’y trouvaient) ; tous les autres fruits étaient verreux.

  The second sentence is correct.

This is an error only on the basis of retaining the most common possibility of what can be said using these words.

The error could be in the choice of the article; if the article "les" is replaced by "des" then you get a sentence that a lot of people find acceptable in the spoken language; it is not proper in formal language.

• Ils en ont mangé des pommes ! or Ils en ont mangé des pommes.

Its meaning can be "They ate a lot of apples." or simply "I assure you that they ate apples.". Necessarily, the discussion preceding this enonciation must have been about people eating apples; you can’t just start talking using it.

This repetition of "pomme" by means of the pronoun "en" is a case of "redondance expressive"; it is treated in "Le Bon Usage, 14th edition" § 373, p. 465. This turn involving repetition is contested by certain people and found to be inelegant by others, although not so much in this particular case.

En doesn’t only refer to indirect objects of the verb (and indefinite direct objects), but also to noun complements of the direct object of the verb.

For example, "J’ai lavé la moitié la plus sale de ma lessive" (I washed the dirtiest half of my laundry) has "la moitié la plus sale de ma lessive" as its direct object, which itself is composed of main noun phrase (la moitié la plus sale) and a complement prepositional phrase (de ma lessive). You can extract this complement phrase from the direct object phrase and turn it into a pronoun attached to the verb:

J’ai lavé la moitié la plus sale de ma lessive

J’en ai lavé la moitié la plus sale (I washed the dirtiest half of it or more idiomatically, I washed its dirtiest half)

It’s likely that it is what’s happening in the question’s sentence, although it’s not obvious without context what this noun complement would be. But let’s invent an example to clarify the transformation at work here:

J’ai mangé les pommes de ton verger

J’en ai mangé les pommes

And it might become obvious that the difference between "j’en ai mangé les pommes" and "j’ai mangé les pommes" is identical to that between "I ate the apples" and "I ate its apples" in English.

The past tense has no influence of this, the same distinction would be obtained the same way with another tense, simple or compound:

J’en mangerai les pommes (I’ll eat its apples)

Je mangerai les pommes (I’ll eat the apples)