Can't put baby in Moses basket during the day

Hello! I adore cuddles with my little boy it is amazing and he is growing so quick and is now just over 12 weeks. 
Does anyone else fine during the day their baby won't go down into the Moses basket/bassinet?  I normally cuddle him to sleep on me in the day then attempt to put him in and he is immediately like no! Occasionally he may stay down asleep but in the main he starts crying until we pick him up again(I could never leave him crying and upset) I can wear a sling to do stuff around the house but just wondering if reinforcing bad habits by picking him up when he gets upset in the Moses basket or is it fine?  Do babies normally grown out of this? Also a really strong startle reflex which we swaddle him for at night!
I know he is only a baby so you can't really reinforce bad habits and couldn't leave him distraught either!
Thank you!