It's a difficult one to answer because Hubspot is a continuously evolving platform. What isn't working so well today will be great tomorrow. The speed at which they are developing is mind blowing. I've been watching this now for 1.5 years and it's pretty amazing.
They're doing some pretty cool stuff and constantly pushing the boundaries, I wouldn't want to single any one thing out, none that might not be 100% of the parts will remain so. I just don't know in which order they develop but I know they have a team behind every aspect and like I said keep evolving the product.
So if the question comes of whether it'll be a problem because perhaps there is something that another software might be better in, it won't be long before that's no longer true. Buying into Hubspot means buying into constant change and evolution - that by itself could be a bit of an issue for some people but in my books that's their greatest plus, despite the constant learning curve.
Although my answer doesn't revolve around a particular feature that is vulnerable, I think my answer will still prove helpful.
Hubspot is weakest concerning their pricing. They essentially ignore small businesses with their high pricing structure.
Mike Volpe, their CMO, basically admits this during his interview with me: https://www.growthhacker.tv/mike-volpe
That being said, I think that they are incredibly wise in regards to their pricing. Big companies have money. Big companies require less customer support. And higher margins allow them invest in the future instead of scraping my now.
Still, this is their weakness. It was also the weakness of KISSmetrics and Mixpanel appeared.
I did an appraisal of HubSpot and wrote it up as a slide deck
It shows where alternate offerings can be used (many free). These are where Hubspot is most vulnerable to competition.
Happy to discuss further