Which characters who have made reference to the "inferior connections" of the Bennet sisters have indicated that these connections have a negative effect on their eligibilty?

I think all the characters are aware of what is at play here. Mr. Darcy has openly commented on the family's "poor connections". He struggles to come to terms with his love for Elizabeth and the Bennet social stature. In the end Mr. Darcy does overcome his prejudices because he truly loves the fiery Elizabeth.