[BioC] Affymetrix internal control up-regulated, is anything wrong?

[Michele Bellesi [guest]]

I am a very beginner with array data analysis.
I have 3 groups CTR and TREATMENT1 and TREATMENT2. I used a very simple design to perform the 3 comparisons, but I found that  2 out 3 Affymetric probesets for actin beta resulted up-regulated in the CTR condition. All the other probsets for actin beta don't significantly change.
Is that normal? could it be a sign of something wrong either during the hybridization or during the analysis? 
Thanks

 -- output of sessionInfo(): 

eset = exprs(expr)[, c(1:18)]

designM = model.matrix(~ 0 + factor(c("C", "C", "C", "C", "C", "C", "T1", "T1", "T1", "T1", "T1", "T1", "T2", "T2", "T2", "T2", "T2", "T2"), levels = c("C", "T1", "T2")))
colnames(designM) = c("C", "T1", "T2")
fit <- lmFit(eset, designM)
contrast.matrix <- makeContrasts(C-T1, C-T2, T1-T2, levels = designM)

fit2 <- contrasts.fit(fit, contrast.matrix) 
fit2 <- eBayes(fit2) 

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