Yeah, just like LH's "lactose-free" meal would include zucchinis, it was to be expected, that A3's "lactose-free" meal would include ...tomatoes (or tomato sauce).
The choice of the special meal will always result in the precise ingredient(s), that cause the issues, to be left out. I had a flight last year, for which I had pre-ordered the "halal" meal and not only did I receive a different main, but also a different dessert. So Aegean will actually take care to eliminate the ingredient(s) from all parts of the meal, however I don't know of an option that would eliminate tomatoes specifically.

What you should have done is to have contacted Aegean well in advance of that flight and let them know of your allergy + intolerance. I have no experience with this, but I have a feeling, that they would have accomodated your request.

fransknorge I don't think anyone likes being served breakfast at 11 a.m., but this isn't even close to the latest this will happen on an Aegean flight, since their cut-off time for breakfast is an 11a.m. scheduled departure (which may as well put the meal service at ...noon!). What Aegean should do is to move the cut-off to 10a.m. departures (at least for international flights), but I think we could make an assumption on why they haven't / won't...

Anyway, here's a picture of that crepe you mentioned from the SKG-DUS flight just the day before your flight

This was pre-ordered about a month ago. In contrast to what has been written here about the whole wheat crepe, this was actually very tasty .