The first unit taught in Pre-Algebra in my district is functions. The way the unit was written was to begin by revisiting the previous year's unit on proportional equations graphically with the use of ratio tables. The first struggle I noticed my students had was being taught the procedure of ratio tables, but no conceptually understanding; in other words, students had procedural understanding - use a ratio table to show if one cookie cost 3 dollars, how much 5 cookies cost - but they would increment by ones, rather than multiplying by five because they had no conceptual understanding of what a ratio table was, they simply used it as a T-Table.
The second struggle comes from the over-usage of ratio tables in 7th grade, where all linear equations were proportional, then moving into 8th grade where there is a y-intercept introduced. Students can identify patterns - 5, 10, 15, 20 - as multiples of 5's, even when written in a T-Table of values, but when there is an initial or starting amount which causes the outputs to change to 3, 8, 13, 18 for example, students have lost their ability to find the pattern, even though the outputs change by 5's still. Only a few students when given easy input/output relationships (times 2 plus 1, times 3 minus 1, etc.) have the basic math facts to help them realize the pattern is the multiples of 2/3 minus/plus one.
The third struggle I see in students is the difference between when something has a multiplicative relationship versus an additive relationship. For example, when writing an equation for a function, students don't know whether the relationship between the input and output is additive or multiplicative nor whether the rate of change is additive or multiplicative. Because of this misunderstanding students struggle with slope as they can't remember if it is input over output or output over input - and for that matter WHY is it output over input - because for all they know the relationship is additive and not multiplicative.