I need to buffer a line 1 meter, however when running the buffer tool in QGIS with the end cap style as "flat" I get the result shown below.
What causes this, and how can I fix it?
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As commented, it seems to be a collection of line and not a polyline. I tried to explain in the image below. The first one has a collection of polylines. You can see that when it is a polyline, the buffer stay connected. And when is another line it has a endpoint/cap.
The second sample is when the buffer is checked the dissolve. It looks like your case.
The third sample is a buffer of a unique polyline.
To tranform the multiline layer to a single poly line you can do it manually with the
merge tool in the Advance Digitalization toolbar, or with the function
dissolve (vetor > geoprocessing > dissolve).