Were those land units embarked on naval transports or were they landlubbers ? :)

Do you have a screenshot of that perchance ?

It is a known bug that the effect of the Lighthouse (and the similar Norsemen Legacy Trait) stick with the units after they were embarked.

Yes, I (and I think more people) reported it, hopefully will be fixed soon.

And the AI loves getting the lighthouse. In Civ and here, I try to prioritize it since I prefer naval play, but the AI often grabs it before I can.

From my experience the units don't even have to embark to have the trait, they simply have it (even their mercenaries). 

Two know bugs about combat strength:

1. lighthouse of Alexandra provides +1 bonus to all units;

2. Ancient era narrative events +2 bonus to all units in the whole game play.

An humankind ai coupled with these two features gets +5 bonus against human player, which is insane. Actually that always happens in my game, because military-oriented ai leader tends to do whatever they can to increase combat strength. They will sure also have +2 bonus from ideology and +1 from professional army, maybe +1 from Hittites, and/or +2 from huns on cavalry. Now I just exploits these bugs myself so that I do not feel pissed off when seeing AI's 30+ strength hunnic hordes.

Yes, forced to do the same and even build the lighthouse in my last game. Otherwise the AI will always stack those.