Issue 1:
Tested with Firefox last stable & developer edition (Aurora).

If i open a new tab or one with content, and i drag it away (to open a new window), and move the cursor over Atom it closes.

Here the shell output:

mfkinder@wk-boe001:~$ atom
mfkinder@wk-boe001:~$ [14953:0213/170206:ERROR:browser_main_loop.cc(164)] Running without the SUID sandbox! See https://code.google.com/p/chromium/wiki/LinuxSUIDSandboxDevelopment for more information on developing with the sandbox on.
[14983:0213/170206:INFO:renderer_main.cc(211)] Renderer process started
App load time: 314ms
[14953:0213/170208:INFO:CONSOLE(11)] "activate linter-jshint", source: /home/mfkinder/.atom/packages/linter-jshint/lib/init.coffee (11)
[14953:0213/170208:INFO:CONSOLE(79)] "Window load time: 1688ms", source: file:///usr/share/atom/resources/app/static/index.js (79)
The program 'atom' received an X Window System error.
This probably reflects a bug in the program.
The error was 'BadAtom (invalid Atom parameter)'.
(Details: serial 495 error_code 5 request_code 20 minor_code 0)
(Note to programmers: normally, X errors are reported asynchronously;
that is, you will receive the error a while after causing it.
To debug your program, run it with the --sync command line
option to change this behavior. You can then get a meaningful
backtrace from your debugger if you break on the gdk_x_error() function.)

Here tested with "--safe"

mfkinder@wk-boe001:~$ atom --safe
mfkinder@wk-boe001:~$ [14753:0213/170133:ERROR:browser_main_loop.cc(164)] Running without the SUID sandbox! See https://code.google.com/p/chromium/wiki/LinuxSUIDSandboxDevelopment for more information on developing with the sandbox on.
[14783:0213/170133:INFO:renderer_main.cc(211)] Renderer process started
App load time: 303ms
[14753:0213/170135:INFO:CONSOLE(79)] "Window load time: 1552ms", source: file:///usr/share/atom/resources/app/static/index.js (79)
The program 'atom' received an X Window System error.
This probably reflects a bug in the program.
The error was 'BadAtom (invalid Atom parameter)'.
(Details: serial 448 error_code 5 request_code 20 minor_code 0)
(Note to programmers: normally, X errors are reported asynchronously;
that is, you will receive the error a while after causing it.
To debug your program, run it with the --sync command line
option to change this behavior. You can then get a meaningful
backtrace from your debugger if you break on the gdk_x_error() function.)

OS: Ubuntu 14.10 x64

Plugins installed:

mfkinder@wk-boe001:~$ apm list

Built-in Atom packages (84)

├── archive-view@0.47.0

├── atom-dark-syntax@0.26.0

├── atom-dark-ui@0.47.0

├── atom-light-syntax@0.26.0

├── atom-light-ui@0.41.0

├── autocomplete@0.44.0

├── autoflow@0.22.0

├── autosave@0.20.0

├── background-tips@0.22.0

├── base16-tomorrow-dark-theme@0.25.0

├── base16-tomorrow-light-theme@0.8.0

├── bookmarks@0.35.0

├── bracket-matcher@0.71.0

├── command-palette@0.34.0

├── deprecation-cop@0.36.0

├── dev-live-reload@0.41.0

├── encoding-selector@0.18.0

├── exception-reporting@0.21.0

├── find-and-replace@0.156.0

├── fuzzy-finder@0.65.0

├── git-diff@0.51.0

├── go-to-line@0.30.0

├── grammar-selector@0.45.0

├── image-view@0.49.0

├── incompatible-packages@0.22.0

├── keybinding-resolver@0.27.0

├── language-c@0.38.0

├── language-clojure@0.12.0

├── language-coffee-script@0.39.0

├── language-csharp@0.5.0

├── language-css@0.28.0

├── language-gfm@0.63.0

├── language-git@0.10.0

├── language-go@0.21.0

├── language-html@0.29.0

├── language-hyperlink@0.12.2

├── language-java@0.14.0

├── language-javascript@0.56.0

├── language-json@0.12.0

├── language-less@0.24.0

├── language-make@0.13.0

├── language-mustache@0.11.0

├── language-objective-c@0.15.0

├── language-perl@0.10.0

├── language-php@0.20.0

├── language-property-list@0.8.0

├── language-python@0.32.0

├── language-ruby@0.48.0

├── language-ruby-on-rails@0.18.0

├── language-sass@0.34.0

├── language-shellscript@0.12.0

├── language-source@0.9.0

├── language-sql@0.14.0

├── language-text@0.6.0

├── language-todo@0.16.0

├── language-toml@0.15.0

├── language-xml@0.28.0

├── language-yaml@0.22.0

├── link@0.30.0

├── markdown-preview@0.134.0

├── metrics@0.42.0

├── notifications@0.27.0

├── one-dark-syntax@0.3.0

├── one-dark-ui@0.4.0

├── one-light-syntax@0.3.0

├── one-light-ui@0.3.0

├── open-on-github@0.32.0

├── package-generator@0.37.0

├── release-notes@0.48.0

├── settings-view@0.178.0

├── snippets@0.72.0

├── solarized-dark-syntax@0.32.0

├── solarized-light-syntax@0.19.0

├── spell-check@0.54.0

├── status-bar@0.59.0

├── styleguide@0.44.0

├── symbols-view@0.82.0

├── tabs@0.65.0

├── timecop@0.29.0

├── tree-view@0.154.0

├── update-package-dependencies@0.8.0

├── welcome@0.21.0

├── whitespace@0.28.0

└── wrap-guide@0.31.0

/home/mfkinder/.atom/packages (11)

├── atom-auto-uglify@0.4.0

├── autocomplete-paths@1.0.2

├── autocomplete-plus@2.1.6

├── git-blame@0.4.0

├── git-log@0.2.0

├── git-tab-status@1.5.3

├── language-mason@2.0.0

├── linter@0.11.1

├── linter-jshint@0.1.0

├── seti-ui@0.6.3

└── tabs-to-spaces@0.8.1

Issue 2:
Atom Version: 0.129.0

Video of me triggering the bug: http://ara.sh/private/atom-crash.ogv

Reproducible every time.

Environment:

Ubuntu 14.04 (all updates installed as of filing this issue)

Unity desktop environment

Repro steps:

Launch atom from the Terminal

Open a Firefox window (or use an existing one)

Drag the Firefox tab anywhere over the Atom window

Actual behavior:

It crashes

Expected behavior:

Not crash :-)

Additional Information:

The terminal prints out the following after the crash:

[7950:0920/180947:ERROR:browser_main_loop.cc(161)] Running without the SUID sandbox! See https://code.google.com/p/chromium/wiki/LinuxSUIDSandboxDevelopment for more information on developing with the sandbox on.
[7950:0920/180947:ERROR:browser_main_loop.cc(189)] GTK theme error: Unable to locate theme engine in module_path: "pixmap",
ATTENTION: default value of option force_s3tc_enable overridden by environment.
App load time: 88ms
[7984:0920/180947:INFO:renderer_main.cc(227)] Renderer process started
[7950:0920/180948:INFO:CONSOLE(18)] "Window load time: 778ms", source: /opt/atom/resources/app/src/window-bootstrap.js (18)
The program 'atom' received an X Window System error.
This probably reflects a bug in the program.
The error was 'BadAtom (invalid Atom parameter)'.
(Details: serial 1360 error_code 5 request_code 20 minor_code 0)
(Note to programmers: normally, X errors are reported asynchronously;
that is, you will receive the error a while after causing it.
To debug your program, run it with the --sync command line
option to change this behavior. You can then get a meaningful
backtrace from your debugger if you break on the gdk_x_error() function.)