I have kept 3 beautiful rabbits throughout my life and everyone of them has been given a good quality life in terms of accomdation, attention and diet. All of them (2 males and 1 female) have made little squeeky noises (nothing alarming) simply when exploring.
Simba is the only bun I have ever had that has needed medication. She makes little stressed noises when having her bayril. With metacam, she makes little happy noises and begs for more!
You learn to tell what the noises mean, I think. But if you are undecided and concerned, get along to a vet for sure.