Your miter limit is interacting with smooth/auto nodes in an unpredictable way. The solutions are to change all the segments to straight lines, change all the nodes to cusp, or hunt down the one or two nodes that are smooth but almost not, i.e. the node control handles are just barely sticking out, and change them to cusp. I used each method on each arrow. The first two fix all the problems but the arrow tip gets pointy. You can see there are still some calculation errors in the last one ...
The fix is easy and the reason is clear but it's probably a bug that should be fixed and may be known. Please note this is not really a problem with the geometry, but a problem in how accurately Inkscape renders geometry.

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My best suggestion is to do it way old school and use a separate filled object for stroke and fill. That is duplicate each arrow remove the stroke from one and the fill from the other, and do stroke to path on the latter. Should work on these and if not then the problem will be static and easy to see.

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Your mind is what you think it is.