Partitions and Bell numbers
Say that a partition of $[n]$ is good if it has no singleton blocks and bad otherwise. $B_n$, the $n$-th Bell number, is the total number of partitions of $[n]$. If $b(n)$ is the number of bad partitions of $[n]$, $F(n)=B_n-b(n)$. As usual, a little data can’t hurt. By direct enumeration of $F(n)$ and $b(n)$ and a table of the Bell numbers I find
$$\begin{array}{cccc} n&F(n)&b(n)&B_n\\ \hline 0&0&1&1\\ 1&0&1&1\\ 2&1&1&2\\ 3&1&4&5\\ 4&4&11&15\\ 5&11&41&52\\ 6&41&162&203 \end{array}$$
This very strongly suggests that $F(n+1)=b(n)$ for $n\ge 1$. To see why this is true, suppose first that $\pi$ is a bad partition of $[n]$; then we can form a good partition of $[n+1]$ by gathering all of the singletons of $\pi$ into a single block and putting $n+1$ into that block. Conversely, if $\pi$ is a good partition of $[n+1]$, we can form a bad partition of $[n]$ by taking the block of $\pi$ containing $n+1$, throwing away $n+1$, and converting the rest of the block to singletons. These operations are clearly inverses of each other and thus establish a bijection between bad partitions of $[n]$ and good partitions of $[n+1]$.
This immediately gives us the recurrence $F(n+1)=B_n-F(n)$. Unwrapping the recurrence, we find that:
$$\begin{align*} F(n+1)&=B_n-F(n)\\ &=B_n-\big(B_{n-1}-F(n-1)\big)\\ &=B_n-B_{n-1}+F(n-1)\\ &=B_n-B_{n-1}+\big(B_{n-2}-F(n-2)\big)\\ &=B_n-B_{n-1}+B_{n-2}-F(n-2)\\ &\;\vdots\\ &=\sum_{i=0}^k(-1)^iB_{n-i}+(-1)^{k+1}F(n-k)\\ &\;\vdots\\ &=\sum_{i=0}^{n-1}(-1)^iB_{n-i}\;. \end{align*}$$
Added: For the first question, let $\pi$ be a good partition of $[n+1]$, and let $B$ be the block containing $n+1$. There is at least one element of $[n]$ in that block, so $[n]\setminus B$ is a proper subset of $[n]$. If $|[n]\setminus B|=k$, $\pi\setminus\{B\}$ can be any one of the $F(k)$ good partitions of $[n]\setminus B$. Conversely, all good partitions of $[n+1]$ can be obtained by choosing a proper subset $S$ of $[n]$, forming a good partition of $S$, and adding to it the block $\{n+1\}\cup([n]\setminus S)$. Since $[n]$ has $\binom{n}k$ subsets of cardinality $k$, $[n+1]$ has $\binom{n}kF(k)$ good partitions in which the block containing $n+1$ has $n-k$ other elements, and it follows that $$F(n+1)=\sum_{k=0}^{n-1}\binom{n}kF(k).$$
It is somewhat surprising that there was no answer in terms of generating function as these are quite straightforward. The species of set partitions is given by $$\mathfrak{P}(\mathfrak{P_{\ge 1}}(\mathcal{Z}))$$ and hence it has the exponential generating function $$G(z) = \exp(\exp(z)-1).$$ The species of set partitions excluding singletons is $$\mathfrak{P}(\mathfrak{P_{\ge 2}}(\mathcal{Z}))$$ and hence it has the exponential generating function $$H(z) = \exp(\exp(z)-1-z).$$ To answer the first question differentiate $H(z)$ to get $$H'(z) = H(z) \times (\exp(z)-1).$$ Here is a useful observation which I have included in several of my posts. When we multiply two exponential generating functions of the sequences $\{a_n\}$ and $\{b_n\}$ we get that $$ A(z) B(z) = \sum_{n\ge 0} a_n \frac{z^n}{n!} \sum_{n\ge 0} b_n \frac{z^n}{n!} = \sum_{n\ge 0} \sum_{k=0}^n \frac{1}{k!}\frac{1}{(n-k)!} a_k b_{n-k} z^n\\ = \sum_{n\ge 0} \sum_{k=0}^n \frac{n!}{k!(n-k)!} a_k b_{n-k} \frac{z^n}{n!} = \sum_{n\ge 0} \left(\sum_{k=0}^n {n\choose k} a_k b_{n-k}\right)\frac{z^n}{n!}$$ i.e. the product of the two generating functions is the generating function of $$\sum_{k=0}^n {n\choose k} a_k b_{n-k}.$$
Therefore when we extract coefficients from the differentiated equation for $H(z)$ we get $$F(n+1) = \sum_{k=0}^{n-1} {n\choose k} F(k) \times 1 = \sum_{k=0}^{n-1} {n\choose k} F(k).$$ The upper limit is $n-1$ and not $n$ because $\exp(z)-1$ has no constant term. This is valid for $n\ge 1.$ The base cases are $F(0)=1$ and $F(1)=0.$
For the second part of the question rewrite the equation for $H(z)$ like this: $$H(z) = \exp(\exp(z)-1)\exp(-z).$$ Using the convolution of exponential generating functions one more time and recognising $G(z)$ from above we obtain that $$F(n) = \sum_{k=0}^n {n\choose k} B_k (-1)^{n-k} = (-1)^n \sum_{k=0}^n {n\choose k} (-1)^k B_k.$$
Here is some Maple code to explore these numbers.
with(combinat, bell); with(combinat, setpartition); nsb := proc(n) option remember; local p, admit, s, res, k; res := 0; for p in setpartition([seq(k, k=1..n)]) do admit := true; for s in p do if nops(s) = 1 then admit := false; break; fi; od; if admit then res := res+1; fi; od; res; end; F := proc(n) option remember; if n=0 then return 1 fi; if n=1 then return 0 fi; add(binomial(n-1, k)*F(k), k=0..n-2); end; q := n -> (-1)^n*add(binomial(n, k)*(-1)^k*bell(k), k=0..n);