I understand you to be saying that your Mongo DB column can contain multiple values which are comma-separated. For example, the string "1001,100" represents a set of values, 1001 and 100. You want to search for a particular value, such as 100, in the column, but only a complete value, not a partial value, should be counted as a match.
If I have understood correctly, then in your regular expression you need to declare that the value you are searching for is a complete value, not a partial value. You do this by adding a word boundary at the start and end of the value:
\b100\b
This will cause the search to match only complete values.
The reason this works is that the \b operator matches a word boundary. A word boundary is a place in the input where there is a word element on one side of the boundary and a non-word element on the other side. So \b100\b will only match when the 100 has non-word elements on both sides – in your case, commas or the beginning or end of the field.