A very commonly used consistent but biased estimator used is that of the estimated standard deviation.
If we are looking at a simple situation in our data is distributed as $x_i \sim N(\mu, \sigma^2)$, then sometimes the MLE estimate of $\sigma$ is used, ie
$\hat \sigma^2 =
\frac{1}{n} \sum_{i = 1}^n (x_i - \bar x)^2$
This is, of course, a biased but consistent estimator of the variance. Some people may try to account for this bias by using
$\hat s^2 =
\frac{1}{n-1} \sum_{i = 1}^n (x_i - \bar x)^2
$
which is now unbiased for $\sigma^2$...but people don't usually look at variances, they usually look at standard deviations! Jensen's inequality will tell us that if $\hat s^2$ is an unbiased estimator of $\sigma^2$ with positive variance, then $E[s] > \sqrt{E[s^2]}$...so even though we had a unbiased estimator for $\sigma^2$, by taking the square root of this estimator, we now have a biased estimator for $\sigma$!
More generally (and stated without proof), it is very common that MLE estimates of variance components will be downwardly biased but consistent. Hopefully, this bias is ignorable; in the example above, we can see that the fix is almost inconsequential for decent sized $n$. However, if the number of parameters estimated becomes very large, it is quite possible that this bias can be especially problematic; this manifests itself as overfitting.