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Yes, this has happened to me. More than once.
After closely examining the fields sorted on, it was resolved.
For instance there are two author fields. One that is used to display and one that is use for sorting. You need to examine and confirm that both are correct.
There may be characters embedded in fields that look the same but have different numeric values, and so sort differently.
There may be spaces or punctuation that differ in ways that are hard to notice.
At no time have I experienced a bug in calibre that cause the sorting to be off. It has always been a correct sort, but perhaps not always the immediate expected sort. What you think you see is not always what is there.
One good way to fix this is to copy/paste fields and/or edit fields for several books at once, as a group.
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