Actually just a bug - normally when a flashcard is created from multiple entries that disagree on a particular field, we blank that field (rather than, say, showing a pronunciation or traditional version or whatever with a meaning it doesn't belong with) and instead embed it in the flashcard definition - if you edit the text of that card you'll see some 'py:zuan4jie4'{.-w_zho .-se} code, which is why you're seeing something that looks like two separate definitions in the "Flashcards" section despite it actually being a single card.
This generally isn't an issue with Pinyin because we split entries with differing Pinyin into different results; however, some dictionaries have buggy enough Pinyin that we set a flag on them to *not* do that (rather than having your search results cluttered with weird / incorrect readings), and HanDeDict is one such dictionary.
To fix this we'll probably either a) add a checkbox so you can override the latter behavior and have Pleco split on HanDeDict entries, or b) take the first Pinyin in cases like this rather than blanking it.