Abstract thinking, understanding the difference between describe and compare, and indicating south on a map tripped up some of last year's matrics.
This is revealed in the department of basic education's diagnostic report, which analyses responses to exam questions.
Now in its seventh year, the report highlights recurring issues: weaker students struggle to read and do basic mathematics, and cannot answer questions that require analytical reasoning or interpretation.
Experts said this pointed to problems in the first three years of learning.
In his state of the nation address on Thursday, President Cyril Ramaphosa said a critical priority was to substantially improve reading comprehension in the first years of school.
"This is essential in equipping children to succeed in education, in work and in life - and it is possibly the single most important factor in overcoming poverty, unemployment and inequality," he said.
The diagnostic report showed pupils had poor mathematical and arithmetical ability, and even poor performance in questions that have appeared regularly in previous examination papers but were phrased differently.
The same reading and reasoning issues were raised in the first report in 2011, which noted "learners' inability to answer questions assessing higher-order thinking skills such as problem solving, critical thinking, analysis and evaluation".
In 2015, the report said poor language skills were a major reason for under-achievement. The latest report said pupils should have a firm understanding of "action verbs used in the phrasing of questions".
Some of the trends that emerged in the 2018 report include: In agricultural sciences, it was noted for the second year in a row that some pupils "cannot confidently handle calculations such as dividing by 1,000 to convert kilograms to tons".
In business studies, many pupils wrote vague and incomplete responses to questions that required full sentences and pupils confused the word "excess" with "interest". The report suggested that deeper thinking skills should be developed during teaching and learning.
Wits professor Leketi Makalela, founding director of the Hub for Multilingual Education and Literacies, said matric was too late to fix these problems.
"Children are not taught higher-order thinking in the first three grades and then we expect them to do it in matric."
As children learnt to read, he said, they should be answering questions about what they read.
"We emphasise mechanical reading and children are memorising sounds that mean nothing to them."
Stellenbosch University education economist Nic Spaull has called for the expansion of promising programmes such as the Early Grade Reading Study.
Piloted in the North West and Mpumalanga, this introduced reading coaches in the first three grades of primary school.
"In schools that received this, there was a 40% improvement in reading outcomes within two years as compared to control schools."
Spaull said that with a "small army" of coaches, resources and lesson plans, half of all primary schools could be reached within eight years at an annual cost of R1.3bn.
Education department spokesperson Elijah Mhlanga said a great deal had been done to improve early grade literacy and numeracy skills.
"The Read to Lead campaign has been mobilising learners, teachers and communities around the importance of reading."..