This happens occasionally to me. I switch virtual spaces, and a Chrome window [usually gmail] *also* moves spaces. 

I set breakpoint for the browser process on
  breakpoint set -name "-[NSApplication activateIgnoringOtherApps:]"
  breakpoint set -name "-[NSWindow makeKeyAndOrderFront:]"

The former is not hit, but the latter is on changing spaces:
"""
(lldb) bt
* thread #1: tid = 0x2b23b0, 0x00007fff937c2f0c AppKit`-[NSWindow makeKeyAndOrderFront:], name = 'CrBrowserMain', queue = 'com.apple.main-thread', stop reason = breakpoint 3.1
  * frame #0: 0x00007fff937c2f0c AppKit`-[NSWindow makeKeyAndOrderFront:]
    frame #1: 0x00007fff938df312 AppKit`-[NSApplication activeSpaceChanged:] + 27
    frame #2: 0x00007fff95aef50c CoreFoundation`__CFNOTIFICATIONCENTER_IS_CALLING_OUT_TO_AN_OBSERVER__ + 12
    frame #3: 0x00007fff95aef40b CoreFoundation`_CFXRegistrationPost + 427
    frame #4: 0x00007fff95aef172 CoreFoundation`___CFXNotificationPost_block_invoke + 50
    frame #5: 0x00007fff95aac5a3 CoreFoundation`-[_CFXNotificationRegistrar find:object:observer:enumerator:] + 1827
    frame #6: 0x00007fff95aab5dc CoreFoundation`_CFXNotificationPost + 604
    frame #7: 0x00007fff974cf997 Foundation`-[NSNotificationCenter postNotificationName:object:userInfo:] + 66
    frame #8: 0x00007fff938df2e5 AppKit`spacesNotificationHandler + 119
    frame #9: 0x00007fffa7754c06 SkyLight`(anonymous namespace)::notify_datagram_handler(unsigned int, CGSDatagramType, void*, unsigned long, void*) + 870
    frame #10: 0x00007fffa7604519 SkyLight`CGSDatagramReadStream::dispatch_next_main_queue_datagram() + 283
    frame #11: 0x00007fffa76043e9 SkyLight`___ZN21CGSDatagramReadStream35dispatch_main_queue_datagrams_asyncEP16dispatch_queue_sPS__block_invoke + 55
    frame #12: 0x00007fffab20f524 libdispatch.dylib`_dispatch_call_block_and_release + 12
    frame #13: 0x00007fffab2068fc libdispatch.dylib`_dispatch_client_callout + 8
    frame #14: 0x00007fffab213aac libdispatch.dylib`_dispatch_main_queue_callback_4CF + 925
    frame #15: 0x00007fff95b18c69 CoreFoundation`__CFRUNLOOP_IS_SERVICING_THE_MAIN_DISPATCH_QUEUE__ + 9
    frame #16: 0x00007fff95ad9cbd CoreFoundation`__CFRunLoopRun + 2205
    frame #17: 0x00007fff95ad91c4 CoreFoundation`CFRunLoopRunSpecific + 420
    frame #18: 0x00007fff9503aebc HIToolbox`RunCurrentEventLoopInMode + 240
    frame #19: 0x00007fff9503acf1 HIToolbox`ReceiveNextEventCommon + 432
    frame #20: 0x00007fff9503ab26 HIToolbox`_BlockUntilNextEventMatchingListInModeWithFilter + 71
    frame #21: 0x00007fff935d5e24 AppKit`_DPSNextEvent + 1120
    frame #22: 0x00007fff93d5185e AppKit`-[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 2796
    frame #23: 0x000000010ad66f20 Google Chrome Framework`___lldb_unnamed_symbol92274$$Google Chrome Framework + 64
    frame #24: 0x000000010b1efd6a Google Chrome Framework`___lldb_unnamed_symbol114371$$Google Chrome Framework + 10
    frame #25: 0x000000010ad66e64 Google Chrome Framework`___lldb_unnamed_symbol92271$$Google Chrome Framework + 164
    frame #26: 0x00007fff935ca7ab AppKit`-[NSApplication run] + 926
    frame #27: 0x000000010b2004ce Google Chrome Framework`___lldb_unnamed_symbol114848$$Google Chrome Framework + 286
    frame #28: 0x000000010b1feecc Google Chrome Framework`___lldb_unnamed_symbol114805$$Google Chrome Framework + 92
    frame #29: 0x000000010b2215a3 Google Chrome Framework`___lldb_unnamed_symbol115616$$Google Chrome Framework + 51
    frame #30: 0x000000010ad6cc95 Google Chrome Framework`___lldb_unnamed_symbol92321$$Google Chrome Framework + 181
    frame #31: 0x0000000109bffe64 Google Chrome Framework`___lldb_unnamed_symbol26151$$Google Chrome Framework + 52
    frame #32: 0x0000000109c02672 Google Chrome Framework`___lldb_unnamed_symbol26188$$Google Chrome Framework + 18
    frame #33: 0x0000000109bfbeec Google Chrome Framework`___lldb_unnamed_symbol26129$$Google Chrome Framework + 124
    frame #34: 0x000000010ad2338b Google Chrome Framework`___lldb_unnamed_symbol90796$$Google Chrome Framework + 891
    frame #35: 0x000000010c637cfd Google Chrome Framework`___lldb_unnamed_symbol185706$$Google Chrome Framework + 2205
    frame #36: 0x000000010ad22764 Google Chrome Framework`___lldb_unnamed_symbol90790$$Google Chrome Framework + 68
    frame #37: 0x00000001096bc0c8 Google Chrome Framework`ChromeMain + 168
    frame #38: 0x000000010963edc4 Google Chrome Canary`main + 404
    frame #39: 0x00007fffab23c235 libdyld.dylib`start + 1
    frame #40: 0x00007fffab23c235 libdyld.dylib`start + 1
"""

Interestingly enough, Chrome is entirely paused since the browser process is paused, but the window still moves spaces after switchign virtual spaces [but it is not brought to the front]. This seems like it's outside of our control