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These graphics are rendered by a library called "Mermaid". HackMD is probably not the source of the problem. I'd recommend opening a ticket in mermaids bugtracker. What will help immensely in resolving this, is the textual representation of the shown charts.
Strange rendered of flow and sequence diagram by browser which is been documented as supported.
Flow diagram by safari version 11 (and chrome for mac version 62)
line is being overlapped
Sequence diagram by firefox version 56
line is being overlapped by white background of note
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