Organisations said claimants were unaware of any rules they were supposed to have broken while chasing jobs, and that the Department for Work and Pensions (DWP) regime is ineffective and targets the most vulnerable.
Claimants can be penalised if they fail to keep appointments with advisers, or do not meet goals set at meetings, such as attending interviews or applying for a specific number of jobs.
Citizens Advice Scotland (CAS) has called for a review of the regime's purpose and wants an analysis of the reasons behind a huge rise in the number of sanctions applied, and whether they are causing people to go hungry.
The DWP has commissioned a review of the use of sanctions, which have risen rapidly in recent years.
While CAS and other charities say they agree there must be punishments for those who fail to follow the rules, they cite dozens of examples of people unfairly dealt with, or for whom the rules have been inappropriately applied.
They say a deprived area of Glasgow had seen a 400% rise in sanctions.
CAS says that, in one case, a woman in the east of Scotland was expected to be in two places at the same time by different back-to-work schemes. She was warned to expect sanctions when she only attended one of them.
In the west of Scotland, one person was said to have got a job but received a four-week benefit penalty after he stopped looking for work while waiting to start his new post.
In one case a man told a CAS adviser he had no money for food, gas or electricity. However, he was still sanctioned after he failed to keep his mobile phone topped up and could not apply for work.
In its response to the review being carried out by Matthew Oakley, a member of the social security advisory committee, CAS says sanctions should only be applied as a last resort. It also says jobsearch requirements should be meaningful and should genuinely support people to find work. It says communication about the rules is often poor and that most unemployed benefit claimants want to work.
Advisers say they see many people who do not understand what was expected of them or who have had money they relied upon stopped without warning or sufficient explanation.
CAS says people should be entitled to a written warning, formal notification if they are at risk of a sanction, and written notification at least 10 days in advance if their money is to be stopped.
The Scottish Council for Voluntary Organisations (SCVO) has also responded, and outlined a possible alternative and more supportive approach to helping the unemployed.
However, director of public affairs John Downie said: "We have little confidence in this review, since welfare reform to date has been driven by ideology rather than a genuine attempt to improve public services."
SCVO says the sanctions regime is leading to people facing extreme hardship and that 73% of referrals to food banks are for people or families affected by benefit delays and sanctions.
Mr Downie added: "Sanctions work against people moving back into work. They are pushed towards destitution and therefore unlikely to take up opportunities to retrain or access employability support. In dealing with a crisis situation the focus for families will be on trying to access the basics of life - food, shelter, heat - rather than moving back towards employment."
SCVO told the review that savings accrued from sanctions were likely to be negated by rising crime, demand for other services and poorer health and wellbeing.
Beth Reid, head of social policy at CAS, said: "In principle, CAS does not object to the use of sanctions, provided they are applied appropriately, with discretion and as a last resort. But the operation of the sanctions regime is not in line with this.
"There needs to be a fundamental and public review of the purpose of the sanctions regime. This review should examine the reasons behind the huge increase in sanctions in recent months and years and the effectiveness of the current regime in meeting its stated purposes and what, if any, relationship there is between sanctions, food poverty and destitution."
A DWP spokesman said: "People should do everything they can to find work in return for their Jobseeker's Allowance. We make it clear to people what the rules are and that they risk losing their benefits if they don't play by them."
l A report from think-tank Demos will today call for law changes to prevent the breakdown of social networks and promote families living more closely together.