@Joel Cherney is correct
You are in the GREP portion of the search function.
Switching to the Text search is what you need.
For the record - for GREP it is finding regular expressions and period is a wildcard.
You're searching for
. . .
Which is finding [any character][space][any character][space][any character]
Which is why you're finding what you're finding
If you need to find an actual Period (the .]
Then the expression would be
Find
\. \. \.
Replace with
$0
That will find the [period][space][period][space][period]
And replace with
[space][found text]
(where $0= found text]