In addition to the issues mentioned by @C. B. Zeller, (the control group / affiliated service group / related employer group issue is so common!) some what I see:
Disregard for deposit timing, both for deferrals, and
Over contributions thinking it can count towards a future year even though the deposit occurs this year. - think throwing in an extra $100,000 because they have the cash available and want it to grow
As well as disregard for limits, such as depositing up to what they think is the maximum, even though the W-2 compensation they have paid themselves(or a covered spouse) is substantially lower.
Investments in unusual assets with no additional compliance such as an independent appraisal for valuation
Assets/accounts titled to the business rather than the plan name when they were intended to be for the plan
Starting more than one plan every time they get a new account or advisor. Or thinking they have more than one plan when really a new doc with a new account might be a restatement of the older document, but they don't realize it
Compensation not being eligible - thinking that profit and loss is enough, and not having earned income, but still making contributions
Failure to make any contributions - for 5, 10+ years(sometimes nothing beyond the first year) at that point the plan isn't really a plan and should be terminated and closed