When using several R/exams exercises with TikZ plots, I have no problems generating exams in HTML format or for Canvas. However, exactly the same exercises when rendered to PDF show the same plots in different questions. As a simple example, you can use the same exercise twice, e.g., for the automaton exercise shipped with the package:
library("exams")
set.seed(0)
exams2pdf(c("automaton.Rnw", "automaton.Rnw"))
The automaton diagram in the exercise should have a double circle for "A" (the "accepting state" described in the text). However, it has the double circle for "B" (as in the first exercise).
It turns out that this was caused by generating graphics files with the same name in different exercises. Since exams 2.3-5 exams2pdf() had a workaround for resolving these problems but the workaround failed in some situations. I just fixed the problem in version 2.4-0.
Other workarounds include using different names for the TikZ graphics files via include_tikz(..., name = ...) or including the TikZ code as LaTeX in exams2pdf. For the latter the logic.Rnw template contains a worked example that embeds the LaTeX code (rather than generating a graphics file) for exams2nops() output.