The pencil mark was right, but the replacement slat is still a little short. Sometimes the missing wood went away as sawdust: a saw removes a strip of material, not a hairline. That strip is the kerf, and it deserves a place in your layout before you cut the useful piece.
Take an offcut of similar wood and draw a clear, square line across it. Mark the waste side with an X. Secure the scrap on a stable bench with suitable support, keeping hands clear of the cutting path. Wear eye protection and use the same handsaw you intend to use on the actual part.
Make a trial cut just on the waste side of the line, leaving the line on the piece you want to keep. Inspect the result: how wide is the cut, and did it wander towards the mark? The trial is not about chasing a universal kerf measurement. It shows what this saw and your cutting technique are doing in this wood.
Transfer that lesson to the replacement slat. Start on the waste side rather than centring the blade over the pencil line. For a close fit, leave a small allowance and trim or sand back carefully, checking against the opening as you go. Making the part slightly long gives you an adjustment; making it short does not.
For several parts from one strip, avoid drawing end-to-end finished lengths with no room for the cuts between them. A simple approach is to cut one part, then measure the next from the new end after checking that it is square. Fit the first piece before committing the rest of the strip to the same length.
Practical takeaway: make one scrap cut, keep the layout line on the good side, and allow for the wood the saw removes. It is a small habit that can save a perfectly sound crate slat from becoming another offcut.
Hand ToolsCrate RepairsMeasuring