There are four levels in total. To get to the second level, you must
travel directly to the central area upon entrance, without deviating
or back-tracking. Press A on the pink block with writing on and it
On the second level, you need to use Flash on the pink block indicated
on the map below, to get to the next level. On the third level you
must use Strength on the specified block to get to the final room on
the fourth level.
My guess is you backtracked. http://pokemondb.net/maps/abyssal-ruins