First of all, nice to meet you. Kyabje Bokar Rinpoche was my teacher....so we have some small relation, at least.
When these things arise, especially after a retreat or some time when one experiences a sense of progress, this is natural, and it's actually potentially a sign of progress, yes.
My advice, based on everything I've been taught, is to merely note and accept these arisings, don't cling to them, nor push them away, nor even seek to analyze them conceptually. The moment they arise, note the arising-"How interesting!" and then let them be. They are actually self-liberated. They will keep arising for some time, perhaps, or re-arising...but each time they do, just note them and let them be. I know it's not easy, in one sense, especially if they're emotionally-charged, but this has worked for me in some similar situations, over time.
There are other "antidotes" but I'd say those depend on the advice and relation with a good Lama.
I rejoice in your ability to do a one month retreat after only a couple years of formal practice under a teacher. That's great!
May any merit generated by on-line discussion
Be dedicated to the Ultimate Benefit of All Sentient Beings.