There are two sections within Natural HR which contribute to the colours of the items shown on calendars.
1. Timeoff types located under:
Administration > HR > Timeoff management > Timeoff types
Each of thee individual timeoff types can be colour coded when adding a new timeoff type, or by editing an existing timeoff type as shown in this article: https://support.naturalhr.com/article/706-getting-started-timeoff-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 bottom of this article: https://support.naturalhr.com/article/637-choosing-a-colour-and-using-the-colour-picker
Additionally, whilst in the calendar options you might want to reduce the number of items displayed per day to say, 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 "+ X more" button as shown below.
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.