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How recently are we talking here? Any chance you could bisect to the offending commit?

I've done dozens of clean builds going back and I tracked it down to:
Last working commit: 29a3c64
First segfaulting build: 123a60e

I couldn't successfully build the three commits in between the two indicated above, so I can't tell where exactly the problem is.

Updated stacktrace on first segfaulting commit 123a60e:

(gdb) bt
#0  0x00000000000001c1 in ?? ()
#1  0x00007efee23c02b8 in qDeleteAll<QList<QgsSymbolLayerV2*>::const_iterator> (begin=..., end=...) at /usr/include/qt4/QtCore/qalgorithms.h:322
#2  0x00007efee23bed6a in qDeleteAll<QList<QgsSymbolLayerV2*> > (c=...) at /usr/include/qt4/QtCore/qalgorithms.h:330
#3  0x00007efee23b2d7e in QgsSymbolV2::~QgsSymbolV2 (this=0x7efee2d88a60 <QgsCategorizedSymbolRendererV2::sSkipRender>, __in_chrg=<optimized out>)
    at /home/ale/dev/QGIS/src/core/symbology-ng/qgssymbolv2.cpp:255
#4  0x00007efee23c15fe in QgsMarkerSymbolV2::~QgsMarkerSymbolV2 (this=0x7efee2d88a60 <QgsCategorizedSymbolRendererV2::sSkipRender>, __in_chrg=<optimized out>)
    at /home/ale/dev/QGIS/src/core/symbology-ng/qgssymbolv2.h:366
#5  0x00007efeddf135ea in __cxa_finalize (d=0x7efee2d87540) at cxa_finalize.c:56
#6  0x00007efee23a74b3 in __do_global_dtors_aux () from /home/ale/apps/lib/libqgis_core.so.2.13.0
#7  0x00007fff7bf20580 in ?? ()
#8  0x00007efee2d9a73a in _dl_fini () at dl-fini.c:252
Backtrace stopped: frame did not save the PC

I first notice this on master, re-tested now on latest master 4511cc474e5b7 and it still segfaults.

I'm pretty sure it's related to

static QgsMarkerSymbolV2 sSkipRender;

in qgscategorizedsymbolrendererv2.h

It may help to use a local static instead of a global static or some other tricks. I wasn't able to reproduce it quickly.

Pushed a commit to master that prevents from copying QgsSymbolV2 (that would be a possible reason for this crash. In fact I couldn't think of another one).
I would have expected the compiler to fail at the root of the problem but it did not... Maybe it's caused by a python plugin?

The good is that with latest master I can now reproduce it in the Qt-Creator debugger, the bad is that it still segfaults with complete different trace:

0    malloc_consolidate    malloc.c    4157    0x7ffff2f9c8f3    
1    _int_free    malloc.c    4057    0x7ffff2f9d56d    
2    ??            0x7ffff5c331cc    
3    ??            0x7ffff5c3323f    
4    ??            0x7ffff59e9c2b    
5    GDALDriver::~GDALDriver()            0x7ffff5c0c742    
6    GDALDriver::~GDALDriver()            0x7ffff5c0c779    
7    GDALDriverManager::~GDALDriverManager()            0x7ffff5c0ecae    
8    GDALDriverManager::~GDALDriverManager()            0x7ffff5c0ece9    
9    ??            0x7ffff590133a    
10    _dl_fini    dl-fini.c    252    0x7ffff7dea73a    
11    __run_exit_handlers    exit.c    82    0x7ffff2f5a259    
12    __GI_exit    exit.c    104    0x7ffff2f5a2a5    
13    __libc_start_main    libc-start.c    321    0x7ffff2f3fecc    
14    _start            0x4198b9    

I guess that you solved the issue reported here (and maybe also #13986) but there is still something wrong happening.

Disabling all plugins doesn't help.

Just tested with python disabled: still crashing.

Update: testing e6a265c1030bae01aa8d0eca905693e371ff0bd7

CGI still crashes with the same error:

(gdb) bt
#0  0x0000000000000181 in ?? ()
#1  0x00007f5d01f85ebc in qDeleteAll<QList<QgsSymbolLayerV2*>::const_iterator> (begin=..., end=...) at /usr/include/qt4/QtCore/qalgorithms.h:322
#2  0x00007f5d01f84a5e in qDeleteAll<QList<QgsSymbolLayerV2*> > (c=...) at /usr/include/qt4/QtCore/qalgorithms.h:330
#3  0x00007f5d01f78180 in QgsSymbolV2::~QgsSymbolV2 (this=0x7f5d02956a60 <QgsCategorizedSymbolRendererV2::sSkipRender>, __in_chrg=<optimized out>)
    at /home/ale/dev/QGIS/src/core/symbology-ng/qgssymbolv2.cpp:239
#4  0x00007f5d01f871e8 in QgsMarkerSymbolV2::~QgsMarkerSymbolV2 (this=0x7f5d02956a60 <QgsCategorizedSymbolRendererV2::sSkipRender>, __in_chrg=<optimized out>)
    at /home/ale/dev/QGIS/src/core/symbology-ng/qgssymbolv2.h:384
#5  0x00007f5cfdad25ea in __cxa_finalize (d=0x7f5d02955560) at cxa_finalize.c:56
#6  0x00007f5d01f6cbf3 in __do_global_dtors_aux () from /home/ale/apps/lib/libqgis_core.so.2.13.0
#7  0x00007ffe49868810 in ?? ()
#8  0x00007f5d0296873a in _dl_fini () at dl-fini.c:252
Backtrace stopped: frame did not save the PC

Confirmed: thanks!