I did this and it worked for me

1. Forget every bluetooth connection on your Mac.

2. Erase bluetooth list on your QC35 (slide the power button to the right and hold until the voice prompt tells you that the list has been deleted)

3. Switch off your Mac's bluetooth, switch off your QC35s.

4. Switch on your Mac's bluetooth FIRST, then switch on your QC35.

5. Pair them

It worked for me not sure about you. But fingers crossed!

After reading Gummibando's suggestion in the comments I resetted the bluetooth module on the MacBook Pro via:

Hold Shift-Option while clicking on the BT menu bar item > Debug menu > Reset the Bluetooth module

This solved it for me.

If your Bose QC35 headphones are simultaneously connected to your MacBook and iPhone, then whichever device is sending an audio signal through to them will be heard in the headphones.

Now, pausing iTunes on your MacBook only pauses iTunes, it isn't going to pause any other audio - so if your headphones are connected at the time then any other audio will still be heard on your headphones, not on your internal MacBook speakers.

If what you want is for sound effects to not play through your headphones, then you can configure your Sound preferences (System Preferences > Sound) so that sound effects play through your internal speakers, even when your headphones are connected via Bluetooth.

Hope this helps, but if I've misunderstood your problem, perhaps you could clarify your question.

Reset and pair again

Another option you could try is to full reset your bluetooth device list and start again. To do this:

• Slide the power switch to the Bluetooth symbol and hold it there
• After about 10 seconds you should hear "Bluetooth device list cleared"
• Now delete your headphones from the Bluetooth list on your MacBook and iPhone
• Pair your headphones again, but only to your MacBook
• Use your headphones with your MacBook for long enough to feel your issue is resolved
• When satisfied, pair your headphone to your iPhone
• Test to see if the behaviour is now what you expect between both devices

NOTE: I have always found that there are random issues like you're experiencing when multiple devices are simultaneously connected to Bluetooth headphones. For me, I no longer do this - but hopefully you have more success.

Bose Support

It may be worth you checking with Bose Support. I remember reading somewhere that these headphones can have their firmware updated - so perhaps Bose could shed some light on the issue you're having or whether or not there is an update available.

UPDATE: I no longer experience these issues so it was likely fixed by a previous update. Open the "Bose Connect" app on your phone and make sure your firmware is up to date.

When experiencing issues on Mac, open the "Bose Connect" app on your iPhone and connect to your headphones from there (if not already connected).

The app correctly configures the headphones and eliminates all sound issues.

I'm not sure how practical this is (I haven't had the chance to measure CPU usage, etc.), but the below AppleScript will do the job—just replace [YOUR HEADPHONES' NAME] with the actual name of your headphones. This is a modified version of a script from an Apple Support Communities thread.

Save the script below as an application, run it, and add it to your startup items—it should run continuously in the background.

repeat
    set statusOld to checkStatus()
    set statusNew to checkStatus()
    repeat while statusOld is equal to statusNew
        delay 5 --for 5 second checks
        set statusNew to checkStatus()
    end repeat
    if statusNew is true then
        tell application "System Preferences" to activate
        tell application "System Preferences"
            reveal anchor "input" of pane id "com.apple.preference.sound"
        end tell
        delay 0.5
        tell application "System Events" to tell process "System Preferences"
            tell table 1 of scroll area 1 of tab group 1 of window 1
                select (row 1 where value of text field 1 is "Internal Microphone")
            end tell
        end tell
        tell application "System Preferences" to quit
    else
        -- Nothing needs to happen, the device was removed
    end if
end repeat

on checkStatus()
    set bluetoothDeviceName to "[YOUR HEADPHONES' NAME]"
    set myString to do shell script "system_profiler SPBluetoothDataType"

    --initial check if it's not even there
    if myString does not contain bluetoothDeviceName then
        return false
    else

        --find out if connected/disconnected
        set AppleScript's text item delimiters to "name:"
        set myList to the text items of myString --each item of mylist is now one of the devices

        set numberOfDevices to count of myList
        set counter to 1
        repeat numberOfDevices times --loop through each devices checking for Connected string
            if item counter of myList contains bluetoothDeviceName then
                if item counter of myList contains "Connected: Yes" then
                    return true
                else if item counter of myList contains "Connected: No" then
                    return false
                else
                    display dialog "Something went wrong with the script" --this shouldn't happen
                end if
            end if
            set counter to counter + 1
        end repeat
    end if
end checkStatus

You could play with the time between checks (the line with the comment for 5 second checks) to reduce resource consumption.

There are a number of new APIs (especially in AVFoundation) coming to macOS High Sierra that would allow for a much cleaner solution to this problem. If you're comfortable with Swift or Objective-C (or the Cocoa scripting bridge in AppleScript and JXA), I would look into using those APIs instead of this script once High Sierra is released. In particular, Apple's Audio Session Programming Guide and this Stack Overflow post show some techniques of detecting Bluetooth connections using AVAudioSession.