There is no difference in card strength between Omaha and Texas Holdem, so a boat is supposed to beat a flush, unless it is a Straight Flush, of course. Straight flushes are still rare in Omaha, but they are more common than in Texas.
It's hard to tell what exactly happened, without giving us more information about the hand. What was the board? What were your 4 hole cards?
The 2 card rule is commonly forgotten/mistaken by new Omaha players, so Yes—it could have been the culprit. It makes a big difference here. The 2 card rule is extremely simple, but many people get it wrong. They think of it as a limit to play UP TO 2 hole cards, while it's actually a rule to combine EXACTLY 2 of your hole cards and EXACTLY 3 of the community cards. No more and no less. It's not possible to use just 1 of your hole cards plus 4 from the board. It's not possible to play the board (0 of your hole cards + 5 from the board). It's not possible to use 3 hole cards + 2 board cards, or 4 hole cards + 1 board card.
Say for example the board is AAKKQ and you have AJJT. You can't use just one Ace from your cards and the 4 community cards AAKK to make a full house. You have to make a 5 card hand using exactly 2 from yours. Your best possible hand is then JT + AKQ (a straight AKQJT). Second best would be AJ + AAK (trips AAAKJ). Then AT + AAK (trips AAAKT). Then JJ + AAK (two pair AAJJK).
The only way to have a full house on AAKKQ board is AK + AAK, AQ + AAQ, KQ + KKQ, or QQ + AAQ. NB: I use colors here to separate the hole cards from the community ones. You can ignore the suits for this particular example.