Mr. Collins is not the most reliable source in the world. One possibility is that Charlotte said no such thing, but that Mr. Collins had interpreted some more innocent remark that way and had convinced himself that that was what she meant. Or, less likely, he was reporting his own opinion as Charlotte's and for some reason he had convinced himself that it was Charlotte's as well.

Another possibility is that Charlotte might have been defending Lydia (and by extension, Lizzy and Jane) against a charge of "bad blood." (Mr. Collins seems like the sort of person who would believe in bad blood.) It may have seemed to Charlotte to be the lesser of two evils for Mr. Collins to believe that Lydia had been indulged than for him to believe she was naturally bad, a charge that could taint her sisters as well.