Multicollinearity
You could have multicollinearity which can make the variance in the error of estimates of $y$ and $\beta$ a lot different (typically the error in $y$ will have lower relative variance). See for more background: https://stats.stackexchange.com/tags/multicollinearity and https://en.wikipedia.org/wiki/Multicollinearity
Assuming a true linear model $y = X\beta_0 + \varepsilon$, estimate $\hat\beta$ and prediction $\hat y=X\hat\beta$. One can define, with $\lVert.\rVert$ the mean square error norm for example:
- Prediction error: $\lVert y-\hat y\rVert = \lVert X(\beta -\hat\beta)\rVert$ (note this definition omits the part related to the error term )
- Estimation error: $\lVert \beta -\hat\beta\rVert$
Let's express the variation of this prediction error $y-\hat y$ in terms of the estimation error $\beta -\hat\beta$.
$$\begin{array}{}
\text{Var}[{y_k}-{\hat{y_k}}] &=& \text{Var}[\mathbf{X_k}(\boldsymbol{\beta} - \boldsymbol{\hat \beta})] \\
&=& \text{Var}[\sum_{i=1}^n X_{ik}(\beta_i - \hat \beta_i) ] \\
\\ &=& \sum_{i=1}^n X_{ik}^2 \text{Var}[\beta_i - \hat \beta_i] \\ && \quad + \, 2 \sum_\limits{1 \leq i<j\leq n} X_{ik} X_{jk} \text{Cov} [\beta_i - \hat \beta_i,\beta_j - \hat \beta_j] \\
\end{array}$$
This last line has an additional term with covariances. This makes that the error (variance) of $y$ can be a lot different from the error (variance) of $\beta$.
A very common issue is that the $\beta_i$ have a negative correlation (due to a positive correlation between the $X_i$, ie multicollinearity) and the variance of the predictions/estimates of $y$ might be (relatively) much smaller than the variance of the estimates of $\beta$.
Prediction versus Estimation
In addition to the issue of multicollinearity, there might be several other issues. The terms 'prediction' and 'estimation' can be ambiguous.
In this particular question, the terms are linked to the estimation of $y$ versus the estimation of $\beta$. However I can see the estimation/prediction of $y$ in various ways. When we fit data $y_i$ with a curve $\hat y_i$ (like the typical fitting, e.g. as in regression) then the $\hat y_i$ are in my vocabulary estimates of $y_i$ and not predictions of $y_i$.
With prediction, I am thinking about issues like generating prediction intervals (which differ from confidence intervals) or issues like extrapolating curves (e.g. extending trends, predicting new values based on old values).
This prediction of values of $y$ based on estimates of $\beta$ contains the same issue as the multicollinearity explained above, but it is more than that and I feel it is not right to conflate these two. The biggest issue is often the discrepance between 'estimating $y$ versus *estimating $\beta$'. In addition you have the discrepance between 'predicting $y$ versus *estimating $\beta$', which contains 'estimating $y$ versus *estimating $\beta$', but is also more than that (e.g. optimizing different loss functions, reducing the loss of our predictions, according to some loss function, is different from reducing the error of our estimates, according to some probability model/likelihood).