1. The complexity of the product. It's not very intuitive and since it's so complex (a necessary "evil"), there are plenty of ways to get into trouble (mess up billing, MRR, etc.)
2. There are unexpected results that demonstrate to me the product has some loose ends. Some glitches. Not many, but they're there.
3. The integration with NetSuite presents some difficult (unable to overcome so far) problems, such as: USD to CAD transactions, invoices and payments that cannot be corrected, sync issues that are unresolvable (again, so far - and it's been a few months).
4. The amount of time and effort migrating data from FreshBooks and configuring SaaSOptics to work the ways we need it to work. Review collected by and hosted on G2.com.