Yosemite moves all desktops to one display on startup
I am having the same issue and I believe it's a system bug (10.10.1) without any good workarounds.  Even if you have no extra spaces on your secondary display, an extra space will show up on your main display on every reboot.  

I will summarize for you the various approaches I've tried and the results of each.  Only the first one solved it totally for me, but it's not ideal as you have to get used to making your secondary display into the new primary display.

(My two displays are different sizes which limits the ways it can be solved.)


If your secondary display is being seen by your Mac as "primary" (does the boot screen Apple logo first appear here?), then you can use Display preferences, under Arrangement, to move the menubar to your secondary display.  I tried it and it fixes the issue, but now everything defaults to the secondary display.  You will constantly see new notifications, new windows, etc. popping up on the secondary display.  Not ideal but it solved the issue of spaces being pushed over to the main display after every reboot.
If your secondary display is being seen by your Mac as "primary" (does the boot screen Apple logo first appear here?), then maybe you can swap the ports where these displays are plugged in.  I purchased the adapters in order to do this, but it was a total failure for me.  No matter where I plugged in my smaller display, the Mac picked this for the boot screen every time.  I even trashed all display preferences and zapped the PRAM to start fresh... no matter what I tried, the smaller secondary display booted as the primary.  Unless you've set the menubar on this same display in preferences, the bug you're reporting will remain.
On the Apple forum, several users have reported that turning off auto-login solved it entirely.  This trick also failed for me.  The boot process looked nicer as you no longer had to look at desktop pictures shifting around and re-sizing, but after logging in, the root problem of spaces shifting over to one display remained.
Turn off the "displays have separate spaces" item in the Mission Control preferences.  Not a practical solution.  This is like killing the patient to cure the disease.  Clearly there is a bug when using separate spaces that urgently needs to be addressed.
If your two displays are the same size and you don't care which one is primary, then whichever display contains the Apple logo on boot will become your primary display.  Use Display preferences, under Arrangement, to move the menubar to your this display.  Then physically arrange them on your actual computer desk to your liking.  This is the only perfect solution, but obviously works only when you don't care which physical display is set as the primary.




EDIT:

Since posting this answer, I submitted this bug to Apple using my Apple developer account on December 18, 2014.  The current status of my bug report (19299246) is "open".  I will update this answer as I track the bug with Apple.