There are two sections within Natural HR which contribute to the colours of the items shown on calendars.
1. Time off types located under:
Administration -> HR -> Time off management -> Timeoff types
Each of the individual time off types can be colour coded when adding a new time off type, or by editing an existing time off type. More information about adding or editing a time off type can be found in the article - Getting started - Time off types.
2. Other calendar entries located under:
Administration > Company > Options > Calendar options
Other calendar entries include items such as Events, Reminders, Birthdays, Training dates and so on. These are controlled under calendar options and as explained near the end of our Choosing a colour and using the colour picker support article.
Additionally, whilst in the calendar options, you might want to reduce the number of items displayed per day to 4 or 5 entries. This way, if you have 10 employees on holiday across your whole company, the calendar for that day will not stretch too long and look unsightly, as there will now be a " Maximum calendar items per day" option that will allow you to limit how many entries appear on a given day.
Whilst this makes for a much better user experience, it would be worth drawing attention to this with new employees or for those who haven't received system training so that they don't miss anything on the calendar.