First of all, you are not entitled to cast any 3rd level cleric spells at 3rd cleric level. In Pathfinder spell levels and caster levels are not the same. You can cast 2nd level spells at 3rd cleric level and 3rd level spells at 5th.
But there are cases when you can cast domain spells at lower levels than ordinary cleric spells with the same name.
As far as I can see, Pathfinder has taken the domain system from 3.5 unchanged. And in 3.5 cleric spells and domain spells can have different level. For example the Wind Wall spell entry in 3.5 reads:
Level: Air 2, Clr 3, Drd 3, Rgr 2, Sor/Wiz 3
Components: V, S, M/DF
Casting Time: 1 standard action
Range: Medium (100 ft. + 10 ft./level)
Effect: Wall up to 10 ft./level long and 5 ft./level high (S)
Duration: 1 round/level
Saving Throw: None; see text
Spell Resistance: Yes
Thus Wind Wall is 3d level cleric spell but 2nd level Air domain spell.
If you take it to Pathfinder (which I think is right) then the Wind Wall spell will be 3rd level cleric spell and 2nd level Air domain spell.
It means that at 3rd caster level (where you get access to 2nd level spells) you'll be able to memorize Wind Wall into your 2nd level domain slot, but not into any other slot you have. You’ll need WIS 12 (10 + 2nd lev) to be able to do it.
At 5th cleric level (where you get access to 3rd level spells) you’ll be able to memorize it into 2nd level domain slot or into 3rd level basic cleric slot. In the later case you’ll need WIS 13.
Just treat domain spells and cleric spells separately. You can memorize domain spells into domain slots, and only that way, and you can memorize cleric spells into any other slot granted by cleric class levels.