most likely scenario is that when "cleaning" your gravel, much trapped waste gets released into the water column, spiking ammonia.
when cleaning substrate, you must be siphoning out water (with all waste) directly above & at the area disturbed. The amount of your beneficial bacteria will not be able to deal with a huge release of bio waste, because the colonies grow to handle what they're usually fed.
Sand is a better substrate than gravel, as it doesn't trap & hide large amounts of waste. Gravel traps a lot and it is breaking down in the gravel, being quite toxic once released.
when cleaning substrate, you must be siphoning out water (with all waste) directly above & at the area disturbed. The amount of your beneficial bacteria will not be able to deal with a huge release of bio waste, because the colonies grow to handle what they're usually fed.
Sand is a better substrate than gravel, as it doesn't trap & hide large amounts of waste. Gravel traps a lot and it is breaking down in the gravel, being quite toxic once released.