I have my baby in a singlet, onesie and 3.5 tog overnight (room is about 17-18degrees) but she still seems cold and moves all over the cot and has started waking at 5am. Is it safe to put a cotton blanket over the top if tightly tucked in and not too high?

It can be difficult to work out what may be the most appropriate clothing/bedding for baby when sleeping.
Red Nose recommends dressing baby according to the room temperature, rather than trying to modify the room temperature with heating or cooling.

How old is your baby?
Is she rolling yet?
Is the 3.5TOG related to a sleeping bag? ...... With arms in or out?
What makes you think your baby is cold?

Blanket(s) can be used as long as there is no risk of covering head &/or face & they are light weight.
Often once baby is rolling, they may not stay under any blanket, or kick it off & may risk head &/or face covering.
Let me know your responses so I can answer a little more specifically.

Here is some general information from Red Nose about bedding amount.

“Dress baby and use layers as you would dress or use layers yourself: to be comfortable, neither too hot nor too cold.
Dress baby for sleep and add/remove lightweight blankets to ensure baby’s back or tummy feels comfortably warm to the touch.
Remove hats, bonnets, beanies and hooded clothing from baby’s head as soon as baby is indoors.”  -
Always sleep baby with head & face uncovered.
“A good way to check baby’s temperature is to feel baby’s back or tummy (don’t worry if baby’s hands and feet feel cool - this is normal)...................
Consider how many layers that you as the baby’s carer are wearing comfortably.”
https://rednose.org.au/article/bedding-amount-recommended-for-safe-sleep
“As long as baby is put down to sleep on their back, and that baby is dressed appropriately for the room temperature – not overdressed or under dressed – with their head and face uncovered, you can feel reassured that you are protecting baby from overheating.
We don’t believe that it’s necessary to use a room temperature monitor, or to leave the heating or cooling on all night, as long as baby is dressed appropriately for the temperature of the room – not too hot, not too cold.”
https://rednose.org.au/article/how-to-dress-baby-for-sleep