I have not tried other possible end punctuation marks but exclamation points (!) certainly cause trouble. Here is an example (HT to Scrivener support, who helped me diagnose this and produced this example.)

**Input**:

```
$ multimarkdown

* This is a test![^f1]
* And this tests no reference![^f2]
* Here we have a space between the two! [^f3]
* This is an inline footnote![^ We shall see what happens to the entirety of this.]
* And an inline footnote under normal conditions.[^ This should work. ]
* And this is a footnote with a workaround!<!-- -->[^f4]

[^f1]: Referenced footnote.

[^f3]: Second referenced footnote.

[^f4]: It works, but it would be nice for the original parsing problem to be fixed.
```

**Output**:

```
<ul>
   <li>This is a test![<sup>f1</sup>]</li>
   <li>And this tests no reference![<sup>f2</sup>]</li>
   <li>Here we have a space between the two! <a href="#fn:1" id="fnref:1" title="see footnote" class="footnote"><sup>1</sup></a></li>
   <li>This is an inline footnote![^ We shall see what happens to the entirety of this.]</li>
   <li>And an inline footnote under normal conditions.<a href="#fn:2" id="fnref:2" title="see footnote" class="footnote"><sup>2</sup></a></li>
   <li>And this is a footnote with a workaround!<!-- --><a href="#fn:3" id="fnref:3" title="see footnote" class="footnote"><sup>3</sup></a></li>
</ul>

<div class="footnotes">
   <hr />
   <ol>
       <li id="fn:1">
           <p>Second referenced footnote. <a href="#fnref:1" title="return to body" class="reversefootnote">&#160;&#8617;</a></p>
       </li>

       <li id="fn:2">
           <p>This should work. <a href="#fnref:2" title="return to body" class="reversefootnote">&#160;&#8617;</a></p>
       </li>

       <li id="fn:3">
           <p>It works, but it would be nice for the original parsing problem to be fixed. <a href="#fnref:3" title="return to body" class="reversefootnote">&#160;&#8617;</a></p>
       </li>
   </ol>
</div>
```

So the problem appears to be impacting both inline and referenced footnote types, and as to be expected, inserting stuff in between the exclamation point and the footnote reference works.