I work in an EC setting and we have always been taught not to let the babies fall sleep with bottles in their cots as a safe practice. We continue this however I was wondering what is the reason behind not letting them fall asleep with bottles in their cots other than it being a choking hazard.

Many Child Health & Safety Organizations do not recommend babies having a bottle when being placed for sleep.
The issue of baby having a bottle to go to sleep is not part of the Red Nose Safe Sleep guidelines, however, there is consistent information & recommendations to suggest that this may not be good practice.

Choking is of particular concern for babies, especially the very young baby when a bottle is propped.

Raising Children’s Network has the following information:
Dangers of bottle-feeding in bed
If your baby gets used to falling asleep with a bottle in bed, she might depend on it to get to sleep. This can make it more difficult for your child to fall asleep or settle herself independently.

Bottle-feeding in bed also has several risks for your baby.

Choking risks
Babies who fall asleep while bottle-feeding can draw liquid into their lungs. They might then choke on it or inhale it. This is like what happens when you have something ‘go down the wrong way’.
It’s more dangerous for your baby than it is for you, because your baby isn’t as good at waking up if something interferes with breathing.
Although it’s more likely that your baby will cough and be uncomfortable, you might want to avoid the risk altogether.
Tooth decay risk
If your baby falls asleep with a bottle of infant formula, formula might slowly drip into your baby’s mouth, soaking your baby’s teeth and putting him at risk of tooth decay.
Risk of ear infections
If your baby drinks while lying flat, milk can flow into her ear cavity, which can cause ear infections.
https://raisingchildren.net.au/newborns/breastfeeding-bottle-feeding/bottle-feeding/giving-the-bottle#dangers-of-bottle-feeding-in-bed-nav-title