10.11, ToT 479bd3c57da04049e08c6746beee3c43a6ad8604.

Repro:

0. Make sure you have a Chrome App installed. (https://chrome.google.com/webstore/detail/ubiquiti-device-discovery/hmpigflbjeapnknladcfphgkemopofig is one that will work.)
1. Go to chrome://apps/
2. Right click an app, select "Remove from Chromium..."
3. Click the (-) button to minimize the window to the dock.
4. Click the minimized window in the dock.

[51889:1295:1113/190617.339740:FATAL:bridged_native_widget_impl.mm(1245)] Check failed: visible_bridged_children == CountBridgedWindows([window_ childWindows]) (2 vs. 1)
0   libbase.dylib                       0x0000000130baa693 base::debug::StackTrace::StackTrace(unsigned long) + 83
1   libbase.dylib                       0x0000000130baa74d base::debug::StackTrace::StackTrace(unsigned long) + 29
2   libbase.dylib                       0x000000013089a59a base::debug::StackTrace::StackTrace() + 26
3   libbase.dylib                       0x00000001308e1ede logging::LogMessage::~LogMessage() + 142
4   libbase.dylib                       0x00000001308e0cd5 logging::LogMessage::~LogMessage() + 21
5   libviews.dylib                      0x000000016a8d1080 views::BridgedNativeWidgetImpl::NotifyVisibilityChangeDown() + 1952
6   libviews.dylib                      0x000000016a8d087f views::BridgedNativeWidgetImpl::OnVisibilityChanged() + 415
7   libviews.dylib                      0x000000016aa9ebb8 -[ViewsNSWindowDelegate onWindowOrderChanged:] + 40
8   libviews.dylib                      0x000000016a8dfdeb -[NativeWidgetMacNSWindow orderWindow:relativeTo:] + 123
9   AppKit                              0x00007fff891d3fc6 -[NSWindow makeKeyAndOrderFront:] + 106
10  AppKit                              0x00007fff891b66ec _NSCoreDockMessageReceive + 1187
11  HIToolbox                           0x00007fff83e13190 DockCallback(unsigned int, unsigned int, void*, void*) + 2256
12  HIServices                          0x00007fff904e08b1 _DCXMaximizedWindows + 39
13  HIServices                          0x00007fff904e0869 _XMaximizedWindows + 76
14  HIServices                          0x00007fff904d3026 mshMIGPerform + 199
15  CoreFoundation                      0x00007fff853c7f69 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE1_PERFORM_FUNCTION__ + 41