Given this example markdown:

~~~{.cpp}
template <
    typename Mixins
> class Thing : public Mixins... {};

struct FooFunctionality;
struct BarFunctionality;
struct BazFunctionality;

Thing<
    FooFunctionality,
    BarFunctionality,
    BazFunctionality
> thing;

// I hope no one ever writes an if statement like this.
if (
 a
 >
 b
)
{
    bar();
}
    
stream >> a
>> b;

stream >> a
 >> b;
 
stream >> a
  >> b;
  
stream >> a
   >> b;
   
stream >> a
    >> b;
~~~

HTML generated by Doxygen has text block withe the following content:

template <
    typename Mixins
<blockquote>
class Thing : public Mixins... {};
</blockquote>
struct FooFunctionality;
struct BarFunctionality;
struct BazFunctionality;
Thing<
    FooFunctionality,
    BarFunctionality,
    BazFunctionality
<blockquote>
thing;
</blockquote>
// I hope no one ever writes an if statement like this.
if (
 a
<blockquote>
</blockquote>
 b
)
{
    bar();
}
stream >> a
<blockquote>
<blockquote>
b;
</blockquote>
</blockquote>
stream >> a
<blockquote>
<blockquote>
b;
</blockquote>
</blockquote>
stream >> a
<blockquote>
<blockquote>
b;
</blockquote>
</blockquote>
stream >> a
<blockquote>
<blockquote>
b;
</blockquote>
</blockquote>
stream >> a
    >> b;



You can see that any line that starts with a '>' before the tab width is
reached is treated as a block quote (with nesting allowed).


I guess there are 2 possible errors here:
a) Looking for block quotes within a fenced code block should not occur (my preference)
b) Block quote generation within a code fence is incorrect (I don't really know why anyone would want to do this)

I have tested this on both 1.8.5 and 1.8.6