Hi Matt Sh., I'm assuming that, by PhD stream, you mean the one that was recently introduced under MI-4? And the reason for your rejection, I'm assuming, is because they don't recognize your work experience, therefore, not meeting the minimum of one year continuous work experience requirement?
With your application, did you include your TA/RA experience as well (with letters of reference, and everything)? If not, then re-applying with your TA/RA experience properly included may actually be worthwhile. We have found out that they accept TA/RA as paid work experience, so assuming that you have completed at least two years of RA/TA work, then you can easily claim at least one year of work experience through TA/RA (NOC 4122). Say you have done your PhD for 3 years. If there is no gap in your study (important), and if you're fully funded (which is mostly the case for most PhD students), you can easily claim more than 1,950 hours of continuous work experience, provided you can document the total number of hours properly (letters of reference with duty descriptions, funding details, etc).
With the equivalent of continuous full-time one year of TA/RA, a Master's degree [and 17+ years of education], 16 points for IELTS, and 5 adaptability points from previous study (which, once again, we have found out that you do not need to have completed a degree, but rather, just two full-time years in a gprogram), then you should have more than 67 points, even if they do NOT consider your previous work experience in your home country at all (several people [with only TA/RA experience] under these circumstances have gotten positive eligibility review from the CIO).
Another option is obviously to appeal, but then again, for your appeal to have any chance of success, then most likely you would have to submit new information or documentations, which they may or may not accept.
Anyway, you might want to check out the PhD stream thread. You can probably learn a lot by reading some of the posts there (since we actually did learn a lot on how the CIO works, issued PER, assign points, etc)