Good find. The Auto-Organize is a little tooo literal.
If I was you I would submit a bug to support for this one as it really is unexpected behavior.
Here are the notes I created when recreating the issue:
1) put in unknown cd
2) in MMW change track 01 Title to Something Inc (no trailing '.')
3) in MMW change track 02 Title to Something Inc. (trailing '.')
4) Right Click CD and select RIP
Rip CD dialog pops up and shows these tracks to be created ..
C:\My Music\Unknown\Unknown Album (7-22-2015 6-37-49 AM)\01 Unknown - Something Inc.mp3
C:\My Music\Unknown\Unknown Album (7-22-2015 6-37-49 AM)\02 Unknown - Something2 Inc.mp3
That is expected because Something2 Inc..mp3 is not a good name.
5) Click to rip tracks
6) Tracks created filenames (no extra '.') correctly
7) MMW, under Music Note, shows the Titles correctly as
Something Inc
Something Inc.

select the two tracks and Ctrl-R (reorganize) using the default mask of ./<artist> - <title> and click OK
The display of 'New Path' will show that it will create Something2 Inc..mp3 which is incorrect.
Good find. The Auto-Organize is a little tooo literal.
If I was you I would submit a bug to support for this one as it really is unexpected behavior.
Here are the notes I created when recreating the issue:
1) put in unknown cd
2) in MMW change track 01 Title to Something Inc (no trailing '.')
3) in MMW change track 02 Title to Something Inc. (trailing '.')
4) Right Click CD and select RIP
Rip CD dialog pops up and shows these tracks to be created ..
C:\My Music\Unknown\Unknown Album (7-22-2015 6-37-49 AM)\01 Unknown - Something Inc.mp3
C:\My Music\Unknown\Unknown Album (7-22-2015 6-37-49 AM)\02 Unknown - Something2 Inc.mp3
That is expected because Something2 Inc..mp3 is not a good name.
5) Click to rip tracks
6) Tracks created filenames (no extra '.') correctly
7) MMW, under Music Note, shows the Titles correctly as
Something Inc
Something Inc.
8) select the two tracks and Ctrl-R (reorganize) using the default mask of ./<artist> - <title> and click OK
The display of 'New Path' will show that it will create Something2 Inc..mp3 which is incorrect.