EPERM during gulp commands - node.js

Question

I have a gulpfile that I am using together with Browserify, Babelify and BrowserSync to implement my build workflow. However, I am constantly having problems with EPERM errors in Node.js.
I first had an error in my gulp clean task that used rimraf in order to clean my dist directory. The task would occasionaly throw an error (I was not able to reproduce the error 100% of attempts though). The error was an EPERM that complained about the unlink action for ./dist/app.js. I tried using del instead of rimraf and for some reason it helped.
However, if I run gulp watch and something changes , there is very often this error now:
(node:10740) fs: re-evaluating native module sources is not supported. If you are using the graceful-fs module, please update it to a more recent version.
[22:52:35] Using gulpfile D:\Workspace\milestones\gulpfile.js
[22:52:35] Starting 'clean'...
[22:52:35] Finished 'clean' after 4.2 ms
[22:52:35] Starting 'build-persistent'...
[22:52:37] Finished 'build-persistent' after 1.55 s
[22:52:37] Starting 'watch'...
[22:52:37] Finished 'watch' after 92 ms
[BS] Local URL: http://localhost:3000
[BS] External URL: http://192.168.0.108:3000
[BS] Serving files from: ./
[22:52:48] Starting 'clean'...
[22:52:48] Finished 'clean' after 2.77 ms
[22:52:48] Starting 'build-persistent'...
stream.js:74
throw er; // Unhandled stream error in pipe.
^
Error: EPERM: operation not permitted, open 'D:\Workspace\milestones\dist\app.js'
at Error (native)
The full gulpfile may be seen in the gist here.
I am running Windows 10.
Update: The issue seems to be absent when running gulp build and therefore might be caused by BrowserSync.