Thanks for the help guys, I thought that much, riser or extender.
Theres nothing in the slot that would prevent the card from going in, if you look at the first slot on the left of the picture there's another sata module that is the same height as the rectangular one that will prevent fitment too. Like I said its really peculiar and he first time I've encountered this. When I was going ahead with the build I almost pushed too hard in disbelief, I hope nothing is damaged.
Im in Toronto dt, so tomorrow I was thinking of visiting CC and asking for help, in the off chance that somehow I've messed up. Weird, frustrating af and depressing...