It was recently noted by one of our technical team that when setting up Calendar overlays the list of colours available seemed a bit screwed up with the same colour name appearing next to different colours. This issue is a result of the colour palette used to generate the custom Look for all sites in our SharePoint environment and is actually not a currently defined by Microsoft as a bug even though it would be nice to have a bit more clarity and control of how these are determined. So the question was asked ‘can we change these colours?’
I have done some additional research and confirmed that the colours presented to the user for calendars are generated by SharePoint based on the theme selected for the web site (in our case the custom Look) and not immediately customisable for calendars out of the box. Specifically each one of the 9 colours defined comes from the definition of Accent 1-6, Hyperlink, and 2 of the text/background theme colours in the custom Look. This is why the first 6 colours map directly to a colour defined by the accent shown in the SharePoint Color Palette Tool. I think the Hyperlink text/background colours are generated based on the definitions within the custom Look.
There are a number of solutions for implementing customisations but these are point solutions that apply to a specific calendar in a specific site and end users would need to deploy the solution themselves to customise the colours in their calendars. We could possibly look at updating our custom site provisioning app to deploy this customisation with a calendar when the site is first created.
For future reference here a few of possible point solutions (all use a similar approach)…
Kirk's Place 
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