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We got an error message in the SP site which is shown below.

"3099 items (list view threshold is 100000). The number of items in this list is approaching the list view threshold, which is 100000 items. This threshold is the limit at which tasks that cause excessive server load (such as those involving all list items) are prohibited".

The question here is why they are seeing this warning message even though the list items currently are 3099 (which is not at all near to 100000). what is the reason for this.

FYI, we had manually increased the threshold limit to 100000 from the default 5000.

Any help would be greatly appreciated.

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I've confirmed both SharePoint Server 2013 and 2016 display this behavior even when the threshold is set to 100,000 and there's only 4,000 items in a list.

It's likely a bug in SharePoint server. Alternately, Microsoft may have intentionally left the behavior there. They encourage customers to address the root cause of having to increase the threshold instead of raising it.

The List View Threshold only restricts the "number of items that a database operation can involve at one time". It doesn't restrict the number of items in a list or library. Microsoft recommends not increasing the threshold above 5000. In fact, they don't allow you to change it in SharePoint Online.

If you choose to increase the threshold, you can ignore the warning.

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