Two problems exist with Markers. The first is that Markers do not take the color of the stroke. This can be worked around by using the Color Markers to Match Stroke effect, by editing the SVG file with the XML Editor, or adding a custom, pre-colored Marker. An alternative solution is to convert the path with the Markers to a path (Path → Object to Path (Shift+Ctrl+C)). This creates a Group with the Markers converted to separate objects, which can be colored independently.